Activity-based probe compounds, compositions, and methods of use

ABSTRACT

Activity-based probe compounds for use in labeling a cysteine protease are provided. The compounds are targeted to the protease through a specific targeting element. The compounds additionally include a detectable element, such as a fluorescent label, a radiolabel, or a chelator. In some cases, the compounds additionally include a quenching element that is released upon reaction with the protease. Also provided are compositions comprising the compounds and methods for using the compounds, for example in labeling a protease in an animal and in visualizing a tumor in an animal.

CROSS-REFERENCE TO RELATED APPLICATION

This application is a continuation of U.S. patent application Ser. No.14/777,024, filed on Sep. 15, 2015, which is a national stageapplication of PCT International Application No. PCT/US2014/029990,filed Mar. 15, 2014, which claims the benefit of U.S. ProvisionalApplication No. 61/794,296, filed on Mar. 15, 2013, the disclosures ofwhich are incorporated herein by reference in their entireties.

STATEMENT OF GOVERNMENTAL SUPPORT

This invention was made with government support under contract EB005011awarded by the National Institutes of Health. The government has certainrights in the invention.

BACKGROUND OF THE INVENTION

A variety of techniques are currently being developed for use in theareas of molecular imaging and disease monitoring. In particular,optical fluorescence imaging is an approach that is beginning to showpromise as a clinical tool, given its sensitivity, specificity, andnon-invasiveness. The specificity of fluorescent optical probes may insome cases be provided by their biological targets. For example, opticalprobes that are recognized by enzyme targets in a biological sampleoften generate extremely specific signals if the fluorescence of theprobe is only unleashed upon enzymatic reaction. Ideally, thefluorescent portion of the probe remains associated with its enzymatictarget, even after the fluorescent signal has been activated by theenzymatic reaction. Such fluorescent activity based probes (ABPs) havebeen described for protease targets. Blum et al. (2009) PLoS One4:e6374; doi:10.1371/journal.pone.0006374. The ABPs can be distinguishedfrom simple fluorogenic substrates by the permanent covalent bond thatresults from reaction of the ABP with the enzyme's active site catalyticresidue. Although fluorescent substrates may appear to be advantageousdue to the signal amplification resulting from the catalytic turnover bytheir target enzyme, APBs have been found to display increased kineticsof tissue uptake and prolonged retention of probe in the target tissuedue to their covalent modification of the target enzyme.

Among the target enzymes of interest for use with fluorescence-basedoptical probes are proteases, and in particular cysteine proteases. Thecysteine cathepsins are a family of proteases that play important rolesin health and disease. Reiser et al. (2010) J. Clin. Invest. 120:3421-31Although their function has mainly been described as being confined tothe endosomal pathway, evidence is accumulating they are a majorregulators of matrix degradation, suggesting that they also function inan extracellular context. Brömme & Wilson (2011) Role of CysteineCathepsins in Extracellular Proteolysis. Biology of Extracellular MatrixVolume 2 23-51. In addition, members of the cysteine cathepsin familyhave been shown to be major players in the development and progressionof several types of cancer. Mohamed & Sloane (2006) Nat. Rev. Cancer(2006) 6:764-75; Palermo & Joyce (2008) Trends Pharmacol. Sci. 29:22-8.Furthermore, changes in the expression of the endogenous inhibitors ofthe cathepsins, the cystatins, have been observed in cancer. Cox (2009)Cystatins and cancer. Front. Biosci. 14:463-74. These observations, incombination with potential changes in the intra- and extracellularmilieu, stress the importance of tools that allow the direct assessmentof the activity of these proteases in the context of a native tumormicroenvironment. Several ABPs targeting the cysteine cathepsin familyhave been synthesized. Edgington et al. (2011) Curr. Opin. Chem. Biol.15:798-805. In particular, the fluorescently quenched ABPs (qABPs) haveproven to be powerful tools for non-invasive optical imaging of cancerand subsequent characterization of the target cathepsins on ahistological, cellular and protein level. Blum et al. (2007) Nat. Chem.Biol. 3:668-77; Verdoes et al. (2012) Chem. Biol. 19:619-28.

Activity-based inhibitors of dipeptidyl peptidase I based on a2,3,5,6-tetrafluorophenoxyarylmethyl ketone reactive group have beenreported (Deu et al. (2010) Chem Biol. 17:808-819), but these inhibitorswere non-peptidic and did not include a detectable group.

Quenched activity-based peptidic inhibitors for use in the fluorescentimaging of cells containing active proteases such as cathepsin have alsobeen reported. See, e.g., U.S. Patent Application Publication No.2007/0036725. These probes employ an ester-linked acyloxymethyl ketonereactive group to bind to the protease active site. In some cases, theactivity-based fluorescent probes are non-peptidic. See, e.g., PCTInternational Publication No. WO 2012/118715. In some cases, theactivity-based probes are used to radiolabel their target enzymes. See,e.g., PCT International Publication No. WO 2009/124265.

There remains a need in the field, however, for novel activity-basedfluorescent probes of cysteine proteases that have higher cellularuptake, that target a broader spectrum of cysteine protease activities,and that offer increased sensitivity of detection.

SUMMARY OF THE INVENTION

The present invention addresses these and other problems by providingcompounds, compositions, and methods of use of the compounds andcompositions for labeling a cysteine protease.

In particular, according to one aspect of the invention, compounds areprovided as represented by structural formula (I):

wherein

-   L is an ether-linked leaving element;-   T is a targeting element; and-   D is a detectable element.

In some embodiments of the invention, the D group is a fluorescentlabel, a radiolabel, or a chelator.

In specific embodiments, the D group is a fluorescent label, and evenmore specifically is a fluorescein, an Oregon green, abora-diaza-indecene, a rhodamine, or a cyanine label. In even morespecific embodiments, the fluorescent label is a cyanine label, such asCy5.

In some embodiments of the invention, the T group targets the compoundto a cysteine protease. In certain embodiments the T group is anon-peptidic targeting element, such as an element comprising a triazolestructure, including, for example, various specific compounds comprisinga triazole structure. In certain other embodiments, the T group is apeptidic targeting element.

In some compound embodiments, the D-T- group is

wherein L₁ is a linker;

-   AA₁ is an amino acid side chain;-   U is O, N, or S;-   R₁ is alkyl, alkenyl, alkynyl, aryl, aralkyl, heteroaryl,    heteroaralkyl, cycloalkyl, cycloalkenyl, cycloalkylalkyl,    heterocyclyl, heterocyclylalkyl, or a protecting group, and is    optionally substituted with 1 to 3 A groups; and each A is    independently alkyl, alkenyl, alkynyl, alkoxy, alkanoyl, alkylamino,    aryl, aryloxy, arylamino, aralkyl, aralkoxy, aralkanoyl, aralkamino,    heteroaryl, heteroaryloxy, heteroarylamino, heteroaralkyl,    heteroaralkoxy, heteroaralkanoyl, heteroaralkamino, cycloalkyl,    cycloalkenyl, cycloalkylalkyl, cycloalkoxy, cycloalkanoyl,    cycloalkamino, heterocyclyl, heterocyclyloxy, heterocyclylamino,    heterocyclylalkyl, heterocyclylalkoxy, heterocyclylalkanoyl,    heterocyclylalkamino, hydroxyl, thio, amino, alkanoylamino,    aroylamino, aralkanoylamino, alkylcarboxy, carbonate, carbamate,    guanidinyl, urea, halo, trihalomethyl, cyano, nitro, phosphoryl,    sulfonyl, sulfonamido, or azido.

In specific compound embodiments, L₁ is an optionally substituted alkyllinker, wherein each carbon atom is optionally replaced with aheteroatom.

In other specific compound embodiments, AA1 is an aralkyl amino acidside chain, optionally substituted with 1 to 3 A groups.

In still other specific compound embodiments, U is O.

In certain embodiments, the D group is a fluorescent label, aradiolabel, or a chelator.

In specific embodiments, the D group is a fluorescent label, and evenmore specifically is a fluorescein, an Oregon green, abora-diaza-indecene, a rhodamine, or a cyanine label. In even morespecific embodiments, the fluorescent label is a cyanine label, such asCy5.

In some compound embodiments, the L group comprises a quencher, and inmore specific embodiments, L is L₂-L₃-Q, wherein L₂ is a phenoxy group,L₃ is a linker, and Q is a quencher.

In specific embodiments, L is

wherein each Y is independently an electron-withdrawing group orhydrogen.

In more specific embodiments, each Y is independently a halogen orhydrogen, and in even more specific embodiments, L is

and L₃ is an optionally substituted alkyl linker, wherein each carbonatom is optionally replaced with a heteroatom.

In even more specific embodiments, L is

wherein R is a QSY quencher, and n is an integer from 1 to 16.

In preferred embodiments, the QSY quencher is a hydrophilic QSYquencher, and more specifically, the hydrophilic QSY quencher is asulfo-QSY quencher.

In some embodiments of the invention, compounds are provided asrepresented by structural formula (II):

wherein D is a fluorescent label, L₃ is a linker, and Q is a quencher.

In more particular embodiments, compounds are provided as represented bystructural formula (III):

wherein R is a QSY quencher, D is a cyanine dye, and m and n areindependently integers from 1 to 16. The R group may, in some of theseembodiments, be QSY21 or sulfo-QSY21, and the D group may be Cy5.

Specific compound embodiments of the invention include the following:

wherein R=QSY21 and n=6;

R=Sulfo-QSY21 and n=6;

R=QSY21 and n=2; and

R=Sulfo-QSY21 and n=2.

According to another aspect, the invention provides compositions for usein labeling a protease in an animal comprising a compound of the instantdisclosure and a pharmaceutically acceptable carrier.

According to yet another aspect, the invention provides methods oflabeling a protease in an animal comprising the step of: administering acomposition of the instant disclosure to the animal.

The invention still further provides methods of visualizing a tumor inan animal comprising the steps of:

administering a composition of the instant disclosure to the animal, andmeasuring a detectable signal generated in the animal from a reaction ofthe composition with a cathepsin cysteine protease, wherein thedetectable signal is associated with a tumor in the animal.

In specific method embodiments, the detectable signal is a fluorescentsignal. In other specific method embodiments, the fluorescent signal isgenerated at a tumor margin.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1. a) Structures of the qABPs GB137 (1) and the probes 2-8synthesized in this work. b) Labeling profile of probes 1-8 in livingRAW cells at 1 μM. c) Concentration dependent labeling by probes 1 and 8in living RAW cells. d) Total cathepsin labeling intensity of probesprobes 1-8 in living RAW cells relative to 5 μM GB137 (1).

FIG. 2. a) Concentration dependent labeling of RAW cell lysate by probe8 at pH 5.5. b) Labeling time course with 0.5 μM probe 8 in living RAWcells. c) Inhibition of labeling of probes 1 and 8 in living RAW cellsby pretreatment with JPM-OEt (50 μM) and serum stability. d) Live cellfluorescence microscopy of RAW cells exposed to 1 μM probe 8 (top row ofpanels) and co-localization with lysotracker (second row of panels,scale bar 10 μm).

FIG. 3. a) Non-invasive optical imaging time-course of tumor bearingmice injected with probe 8 and 1 (right panels). The lower panelsrepresent the optimal fluorescence contrast at each time point. b)Time-dependent tumor-specific fluorescence (tumor-background) for micetreated with probe 1 or 8 (n=3; data represent mean values±standarderrors). c) Ex vivo tumor fluorescence (top panel) and in vivofluorescently labeled proteins after SDS-PAGE visualized by in-gelfluorescence scanning (lower panel). d) Fluorescence intensity at endpoint of noninvasive optical imaging (shown in a), ex vivo tumorimaging, and in-gel fluorescence labeling (shown in c). Intensityrelative to probe 1 is depicted (n=3; data represent meanvalues±standard errors). e) Fluorescence microscopy of probe 8 (leftpanel) treated tumor tissue section with CD68 immuno-staining (middlepanel) and nuclear staining (DAPI-right panel, scale bar 50 μm). f) 3Dreconstruction of CLSM of probe 8 (Red) treated tumor tissue sectionwith CD68 immuno-staining (Green) and nuclear staining (DAPI-Blue).

FIG. 4. a) Immunoprecipitation of BMV109 labeled cysteine cathepsins.b,c) Concentration dependent labeling by probes 1-8 in living RAW cells.The panels in b) and c) were run on the same gels respectively.

FIG. 5. a) Non-invasive optical imaging of tumor bearing mice 8 hourspost injection of probe 1, 2, 6 or 8. The lower panels represent theoptimal fluorescence contrast at each time point. b) Time-dependenttumor-specific fluorescence (tumor background) for mice treated withprobe 1, 2, 6 or 8 (n=3; data represent mean values±standard errors). c)Ex vivo tumor fluorescence (top panel) and in vivo fluorescently labeledproteins after SDS-PAGE visualized by in-gel fluorescence scanning(lower panel). d) Fluorescence intensity of end point of noninvasiveoptical imaging (shown in a), ex vivo tumor imaging, and in-gelfluorescence labeling (shown in c). Intensity relative to probe 1 isdepicted (n=3; data represent mean values±standard errors). e)Fluorescence microscopy of probe 8 (first, third, and fourth columns)treated tumor tissue section with CD68 immuno-staining (second, third,and fourth columns) and nuclear staining (DAPI-third and fourth columns,scale bar 50 μm). No probe control (middle row panels) and iso-typecontrol for immuno-staining (lower row panels) are depicted). f)Colocalization diagram for probe 8 (Cy5) and CD68 (FITC).

DETAILED DESCRIPTION OF THE INVENTION

The cysteine cathepsins are a family of proteases that play importantroles in both normal cellular physiology as well as in the pathology ofmany human diseases. Therefore, a number of substrate and activity basedprobe (ABP) classes have been developed to study the function of theseenzymes. Provided herein is a class of quenched fluorescentactivity-based probes containing, in some embodiments, a phenoxymethylketone (PMK) electrophile. These reagents show enhanced, broadreactivity towards the cysteine cathepsins resulting in dramaticallyimproved in vitro and in vivo labeling properties compared to previouslyreported ABPs. The probes are further demonstrated herein to highlighttumors in mice with unprecedented signal intensity and contrast. Thesenew reagents enable the study of cysteine cathepsins on the organismal,tissue, cell and protein level in diverse models of human disease.

Compounds

Accordingly, in some aspects, the instant disclosure provides novelcompounds for use in labeling protease enzymes, particularly cathepsins.The compounds of the disclosure may be compounds of the formula (I):

wherein

L is an ether-linked leaving element;

T is a targeting element; and

D is a detectable element.

The targeting element, T, of the instant compounds may be a peptidic ora non-peptidic structure, and it preferably targets the compound to acysteine protease.

Non-limiting examples of non-peptidic structural elements usefullyincorporated into the instant compounds for these purposes are describedin PCT International Publication No. WO2012/118715, which isincorporated herein by reference in its entirety. In preferredembodiments, the non-peptidic targeting element comprises a triazolestructure.

Specific examples of compounds of the invention with non-peptidictargeting elements are:

Non-limiting examples of peptidic structural elements that may beusefully incorporated into the instant compounds for targeting thecompounds to cysteine proteases, and in particular, cysteine cathepsins,are described in PCT International Publication No. WO2009/124265, whichis incorporated herein by reference in its entirety.

In some embodiments of the instant compounds, D-T- is

wherein L₁ is a linker;

AA₁ is an amino acid side chain;

U is O, N, or S;

R₁ is alkyl, alkenyl, alkynyl, aryl, aralkyl, heteroaryl, heteroaralkyl,cycloalkyl, cycloalkenyl, cycloalkylalkyl, heterocyclyl,heterocyclylalkyl, or a protecting group, and is optionally substitutedwith 1 to 3 A groups; and each A is independently alkyl, alkenyl,alkynyl, alkoxy, alkanoyl, alkylamino, aryl, aryloxy, arylamino,aralkyl, aralkoxy, aralkanoyl, aralkamino, heteroaryl, heteroaryloxy,heteroarylamino, heteroaralkyl, heteroaralkoxy, heteroaralkanoyl,heteroaralkamino, cycloalkyl, cycloalkenyl, cycloalkylalkyl,cycloalkoxy, cycloalkanoyl, cycloalkamino, heterocyclyl,heterocyclyloxy, heterocyclylamino, heterocyclylalkyl,heterocyclylalkoxy, heterocyclylalkanoyl, heterocyclylalkamino,hydroxyl, thio, amino, alkanoylamino, aroylamino, aralkanoylamino,alkylcarboxy, carbonate, carbamate, guanidinyl, urea, halo,trihalomethyl, cyano, nitro, phosphoryl, sulfonyl, sulfonamido, orazido.

As used herein, the term “alkyl” refers to the radical of saturatedaliphatic groups, including straight-chain alkyl groups, branched-chainalkyl groups, cycloalkyl (alicyclic) groups, alkyl-substitutedcycloalkyl groups, and cycloalkyl-substituted alkyl groups. In someembodiments, a straight chain or branched chain alkyl has 30 or fewercarbon atoms in its backbone (e.g., C₁-C₃₀ for straight chains, C₃-C₃₀for branched chains), and more specifically 20 or fewer. Likewise, somecycloalkyls have from 3-10 carbon atoms in their ring structure, andmore specifically have 5, 6 or 7 carbons in the ring structure.

Moreover, the term “alkyl” (or “lower alkyl”) as used throughout thespecification, examples, and claims is intended to include both“unsubstituted alkyls” and “substituted alkyls”, the latter of whichrefers to alkyl moieties having substituents replacing a hydrogen on oneor more carbons of the hydrocarbon backbone. Such substituents caninclude, for example, a halo, a hydroxyl, a carbonyl (such as a keto, acarboxy, an alkoxycarbonyl, a formyl, or an acyl), a thiocarbonyl (suchas a thioester, a thioacetate, or a thioformate), an alkoxyl, aphosphoryl, a phosphate, a phosphonate, a phosphinate, an amino, anamido, an amidine, an imine, a cyano, a nitro, an azido, a thio, analkylthio, a sulfate, a sulfonate, a sulfamoyl, a sulfonamido, asulfonyl, a heterocyclyl, an aralkyl, or an aromatic or heteroaromaticmoiety. It will be understood by those skilled in the art that themoieties substituted on the hydrocarbon chain can themselves besubstituted, if appropriate. For instance, the substituents of asubstituted alkyl may include substituted and unsubstituted forms ofamino, azido, imino, amido, phosphoryl (including phosphonate andphosphinate), sulfonyl (including sulfate, sulfonamido, sulfamoyl andsulfonate), and silyl groups, as well as ethers, alkylthios, carbonyls(including ketones, aldehydes, carboxylates, and esters), —CF₃, —CN andthe like. Exemplary substituted alkyls are described below.

Cycloalkyls can be further substituted with alkyls, alkenyls, alkoxys,alkylthios, aminoalkyls, carbonyl-substituted alkyls, —CF₃, —CN, and thelike.

As used herein, the term “alkoxy” refers to an alkyl group, in certainspecific embodiments, a lower alkyl group, having an oxygen attachedthereto. Representative alkoxy groups include methoxy, ethoxy, propoxy,t-butoxy, and the like.

The term “alkenyl”, as used herein, refers to an aliphatic groupcontaining at least one double bond and is intended to include both“unsubstituted alkenyls” and “substituted alkenyls”, the latter of whichrefers to alkenyl moieties having substituents replacing a hydrogen onone or more carbons of the alkenyl group. Such substituents may occur onone or more carbons that are included or not included in one or moredouble bonds. Moreover, such substituents include all those contemplatedfor alkyl groups, as discussed above, except where stability isprohibitive. For example, substitution of alkenyl groups by one or morealkyl, cycloalkyl, heterocyclyl, aryl, or heteroaryl groups iscontemplated.

The term “C_(x-y)” when used in conjunction with a chemical moiety, suchas acyl, acyloxy, alkyl, alkenyl, alkynyl, or alkoxy, is meant toinclude groups that contain from x to y carbons in the chain. Forexample, the term “C_(x-y)-alkyl” refers to substituted or unsubstitutedsaturated hydrocarbon groups, including straight-chain alkyl andbranched-chain alkyl groups that contain from x to y carbons in thechain, including haloalkyl groups such as trifluoromethyl and2,2,2-trifluoroethyl, etc. “C₀-alkyl” indicates a hydrogen where thegroup is in a terminal position, or is a bond if internal. The terms“C_(2-y)-alkenyl” and “C_(2-y)-alkynyl” refer to substituted orunsubstituted unsaturated aliphatic groups analogous in length andpossible substitution to the alkyls described above, but that contain atleast one double or triple bond, respectively.

The term “alkylamino”, as used herein, refers to an amino groupsubstituted with at least one alkyl group.

The term “alkylthio”, as used herein, refers to a thiol groupsubstituted with an alkyl group and may be represented by the generalformula alkyl-S-.

The term “alkynyl”, as used herein, refers to an aliphatic groupcontaining at least one triple bond and is intended to include both“unsubstituted alkynyls” and “substituted alkynyls”, the latter of whichrefers to alkynyl moieties having substituents replacing a hydrogen onone or more carbons of the alkynyl group. Such substituents may occur onone or more carbons that are included or not included in one or moretriple bonds. Moreover, such substituents include all those contemplatedfor alkyl groups, as discussed above, except where stability isprohibitive. For example, substitution of alkynyl groups by one or morealkyl, cycloalkyl, heterocyclyl, aryl, or heteroaryl groups iscontemplated.

The term “amide”, as used herein, refers to a group

wherein R^(x) and R^(y) each independently represent a hydrogen orhydrocarbyl group, or R^(x) and R^(y) taken together with the N atom towhich they are attached complete a heterocycle having from 4 to 8 atomsin the ring structure.

The terms “amine” and “amino” are art-recognized and refer to bothunsubstituted and substituted amines and salts thereof, e.g., a moietythat can be represented by

wherein R^(x), R^(y), and R^(z) each independently represent a hydrogenor a hydrocarbyl group, or R^(x) and R^(y) taken together with the Natom to which they are attached complete a heterocycle having from 4 to8 atoms in the ring structure.

The term “aminoalkyl”, as used herein, refers to an alkyl groupsubstituted with an amino group.

The term “aralkyl”, as used herein, refers to an alkyl group substitutedwith an aryl group.

The term “aryl” as used herein includes substituted or unsubstitutedsingle-ring aromatic groups in which each atom of the ring is carbon. Incertain embodiments, the ring is a 5- to 7-membered ring, and in morespecific embodiments is a 6-membered ring. The term “aryl” also includespolycyclic ring systems having two or more cyclic rings in which two ormore carbons are common to two adjoining rings wherein at least one ofthe rings is aromatic, e.g., the other cyclic rings can be cycloalkyls,cycloalkenyls, cycloalkynyls, aryls, heteroaryls, and/or heterocyclyls.Aryl groups include benzene, naphthalene, phenanthrene, phenol, aniline,and the like.

The term “carbamate” is art-recognized and refers to a group

wherein R^(x) and R^(y) independently represent hydrogen or ahydrocarbyl group, or R^(x) and R^(y) taken together with the atoms towhich they are attached complete a heterocycle having from 4 to 8 atomsin the ring structure.

The term “cycloalkyl”, as used herein, refers to a non-aromaticsaturated or unsaturated ring in which each atom of the ring is carbon.In certain embodiments, a cycloalkyl ring contains from 3 to 10 atoms,and in more specific embodiments from 5 to 7 atoms.

The term “carbonate” is art-recognized and refers to a group—OCO₂—R^(x), wherein R^(x) represents a hydrocarbyl group.

The term “carboxy”, as used herein, refers to a group represented by theformula —CO₂H.

The term “ester”, as used herein, refers to a group —C(O)OR^(x) whereinR^(x) represents a hydrocarbyl group.

The term “ether”, as used herein, refers to a hydrocarbyl group linkedthrough an oxygen to another hydrocarbyl group. Accordingly, an ethersubstituent of a hydrocarbyl group may be hydrocarbyl-O-. Ethers may beeither symmetrical or unsymmetrical. Examples of ethers include, but arenot limited to, heterocycle-O-heterocycle and aryl-O-heterocycle. Ethersinclude “alkoxyalkyl” groups, which may be represented by the generalformula alkyl-O-alkyl.

The term “guanidinyl” is art-recognized and may be represented by thegeneral formula

wherein R^(x) and R^(y) independently represent hydrogen or ahydrocarbyl.

The terms “halo” and “halogen” as used herein mean halogen and includechloro, fluoro, bromo, and iodo.

The terms “hetaralkyl” and “heteroaralkyl”, as used herein, refer to analkyl group substituted with a hetaryl group.

The terms “heteroaryl” and “hetaryl” include substituted orunsubstituted aromatic single ring structures, in certain specificembodiments 5- to 7-membered rings, more specifically 5- to 6-memberedrings, whose ring structures include at least one heteroatom, in someembodiments one to four heteroatoms, and in more specific embodimentsone or two heteroatoms. The terms “heteroaryl” and “hetaryl” alsoinclude polycyclic ring systems having two or more cyclic rings in whichtwo or more carbons are common to two adjoining rings wherein at leastone of the rings is heteroaromatic, e.g., the other cyclic rings can becycloalkyls, cycloalkenyls, cycloalkynyls, aryls, heteroaryls, and/orheterocyclyls. Heteroaryl groups include, for example, pyrrole, furan,thiophene, imidazole, oxazole, thiazole, pyrazole, pyridine, pyrazine,pyridazine, and pyrimidine, and the like.

The term “heteroatom” as used herein means an atom of any element otherthan carbon or hydrogen. Typical heteroatoms are nitrogen, oxygen, andsulfur.

The terms “heterocyclyl”, “heterocycle”, and “heterocyclic” refer tosubstituted or unsubstituted non-aromatic ring structures, in certainspecific embodiments 3- to 10-membered rings, more specifically 3- to7-membered rings, whose ring structures include at least one heteroatom,in some embodiments one to four heteroatoms, and in more specificembodiments one or two heteroatoms. The terms “heterocyclyl” and“heterocyclic” also include polycyclic ring systems having two or morecyclic rings in which two or more carbons are common to two adjoiningrings wherein at least one of the rings is heterocyclic, e.g., the othercyclic rings can be cycloalkyls, cycloalkenyls, cycloalkynyls, aryls,heteroaryls, and/or heterocyclyls. Heterocyclyl groups include, forexample, piperidine, piperazine, pyrrolidine, morpholine, lactones,lactams, and the like.

The term “heterocyclylalkyl”, as used herein, refers to an alkyl groupsubstituted with a heterocycle group.

The term “hydrocarbyl”, as used herein, refers to a group that is bondedthrough a carbon atom that does not have a ═O or ═S substituent, andtypically has at least one carbon-hydrogen bond and a primarily carbonbackbone, but may optionally include heteroatoms. Thus, groups likemethyl, ethoxyethyl, 2-pyridyl, and trifluoromethyl are considered to behydrocarbyl for the purposes herein, but substituents such as acetyl(which has a ═O substituent on the linking carbon) and ethoxy (which islinked through oxygen, not carbon) are not. Hydrocarbyl groups include,but are not limited to aryl, heteroaryl, carbocycle, heterocycle, alkyl,alkenyl, alkynyl, and combinations thereof.

The term “hydroxyalkyl”, as used herein, refers to an alkyl groupsubstituted with a hydroxy group.

The term “lower” when used in conjunction with a chemical moiety, suchas acyl, acyloxy, alkyl, alkenyl, alkynyl, or alkoxy is meant to includegroups where there are ten or fewer non-hydrogen atoms in thesubstituent, and in certain embodiments, six or fewer. A “lower alkyl”,for example, refers to an alkyl group that contains ten or fewer carbonatoms, and in specific embodiments six or fewer carbon atoms. In certainembodiments, the acyl, acyloxy, alkyl, alkenyl, alkynyl, and alkoxysubstituents defined herein are respectively lower acyl, lower acyloxy,lower alkyl, lower alkenyl, lower alkynyl, and lower alkoxy, whetherthey appear alone or in combination with other substituents, such as inthe recitations hydroxyalkyl and aralkyl (in which case, for example,the atoms within the aryl group are not counted when counting the carbonatoms in the alkyl substituent).

The terms “polycyclyl”, “polycycle”, and “polycyclic” refer to two ormore rings (e.g., cycloalkyls, cycloalkenyls, cycloalkynyls, aryls,heteroaryls, and/or heterocyclyls) in which two or more atoms are commonto two adjoining rings, e.g., the rings are “fused rings”. Each of therings of the polycycle can be substituted or unsubstituted. In certainembodiments, each ring of the polycycle contains from 3 to 10 atoms inthe ring, more specifically from 5 to 7.

The term “substituted” refers to moieties having substituents replacinga hydrogen on one or more carbons of the backbone. It will be understoodthat “substitution” or “substituted with” includes the implicit provisothat such substitution is in accordance with permitted valence of thesubstituted atom and the substituent, and that the substitution resultsin a stable compound, e.g., a compound that does not spontaneouslyundergo transformation such as by rearrangement, cyclization,elimination, etc., under conditions in which the compound is to be used.As used herein, the term “substituted” is contemplated to include allpermissible substituents of organic compounds. In a broad aspect, thepermissible substituents include acyclic and cyclic, branched andunbranched, carbocyclic and heterocyclic, aromatic and non-aromaticsubstituents of organic compounds. The permissible substituents can beone or more and the same or different for appropriate organic compounds.For purposes of this invention, the heteroatoms such as nitrogen mayhave hydrogen substituents and/or any permissible substituents oforganic compounds described herein which satisfy the valences of theheteroatoms. Substituents may include any substituents described herein,for example, a halogen, a hydroxyl, a carbonyl (such as a keto, acarboxy, an alkoxycarbonyl, a formyl, or an acyl), a thiocarbonyl (suchas a thioester, a thioacetate, or a thioformate), an alkoxyl, aphosphoryl, a phosphate, a phosphonate, a phosphinate, an amino, anamido, an amidine, an imine, a cyano, a nitro, an azido, a sulfhydryl,an alkylthio, a sulfate, a sulfonate, a sulfamoyl, a sulfonamido, asulfonyl, a heterocyclyl, an aralkyl, or an aromatic or heteroaromaticmoiety. It will be understood by those skilled in the art that themoieties substituted on the hydrocarbon chain may themselves besubstituted, if appropriate.

Unless specifically described as “unsubstituted”, references to chemicalmoieties herein are understood to include substituted variants. Forexample, reference to an “aryl” group or moiety implicitly includes bothsubstituted and unsubstituted variants.

The term “sulfate” is art-recognized and refers to the group —OSO₃H, ora pharmaceutically acceptable salt thereof.

The term “sulfonamide” is art-recognized and refers to the grouprepresented by the general formulae

wherein R^(x) and R^(y) independently represent hydrogen or hydrocarbyl.

The term “sulfoxide” is art-recognized and refers to the group—S(O)—R^(x), wherein R^(x) represents a hydrocarbyl.

The term “sulfo” or “sulfonate” is art-recognized and refers to thegroup —SO₃H, or a pharmaceutically acceptable salt thereof.

The term “sulfone” is art-recognized and refers to the group—S(O)₂—R^(x), wherein R^(x) represents a hydrocarbyl.

The term “thioalkyl”, as used herein, refers to an alkyl groupsubstituted with a thiol group.

The term “thioester”, as used herein, refers to a group —C(O)SRX or—SC(O)R^(x) wherein R^(x) represents a hydrocarbyl.

The term “thioether”, as used herein, is equivalent to an ether, whereinthe oxygen is replaced with a sulfur.

The term “urea” is art-recognized and may be represented by the generalformula

wherein R^(x) and R^(y) independently represent hydrogen or ahydrocarbyl.

The compounds of the instant invention are generally synthesized usingstandard synthetic chemical techniques, for example using the methodsdescribed in the Example section below. Other useful synthetictechniques are described, for example, in March's Advanced OrganicChemistry: Reactions, Mechanisms, and Structure, 7th Ed., (Wiley, 2013);Carey and Sundberg, Advanced Organic Chemistry 4^(th) Ed., Vols. A and B(Plenum 2000, 2001); Fiesers' Reagents for Organic Synthesis, Volumes1-27 (Wiley, 2013); Rodd's Chemistry of Carbon Compounds, Volumes 1-5and Supplementals (Elsevier Science Publishers, 1989); OrganicReactions, Volumes 1-81 (Wiley, 2013); and Larock's ComprehensiveOrganic Transformations (VCH Publishers Inc., 1989) (all of which areincorporated by reference in their entirety). The compounds are normallysynthesized using starting materials that are generally available fromcommercial sources or are readily prepared using methods well known tothose skilled in the art. See, e.g., Fiesers' Reagents for OrganicSynthesis, Volumes 1-27 (Wiley, 2013), or Beilsteins Handbuch derorganischen Chemie, 4, Aufl. ed. Springer-Verlag, Berlin, includingsupplements.

When referring to components of the compounds of the invention, the term“residue derived from” may be used to describe a residue formed by thereaction of a first reactive functional group on a first component and asecond reactive functional group on a second component to form acovalent bond. In exemplary embodiments, an amine group on a firstcomponent may be reacted with an activated carboxyl group on a secondcomponent to form a residue including one or more amide moieties. Otherpermutations of first and second reactive functional groups areencompassed by the invention. For example, the copper-catalyzed orcopper-free reaction of an azide-substituted first component with analkyne-substituted second component results in a triazole-containingresidue through the well-known “click” reaction, as would be understoodby those of ordinary skill in the art. See Kolb et al. (2001) Angew.Chem. Int. Ed. Engl. 40:2004; Evans (2007) Aus. J. Chem. 60:384.Exemplary methods of generating non-peptidic fluorescent imaging probesusing “click” reactions are provided in PCT International PublicationNo. WO 2012/118715. Adaptation of these methods to generate or modifycompounds of the instant claims is within the skill in the art.

One of ordinary skill in the art would understand that a protectinggroup is reversibly attached to a desired position of the molecule tocontrol the reaction of other agents at that position. Protecting groupsuseful in the practice of the instant invention are well known in theart. See, for example, Greene's Protective Groups in Organic Synthesis,4^(th) edition, by P. G. M. Wuts and T. W. Greene (Wiley-Interscience,2006); and Protecting Groups, by P. Kocienski (Thieme, 2005).

The L₁ group of the instant compounds is a linker group that connectsthe detectable element, D, to the targeting element. This group may beany suitable linker, as would be understood by the person of ordinaryskill in the art. The L₁ group is preferably an alkyl linker group,wherein the alkyl linker is optionally substituted, and furthermore,wherein the carbons in the linker are optionally replaced by heteroatomsto the extent that the resulting structure is chemically stable. Suchsubstitutions and replacements should be understood to includeintervening groups within the linker such as ethers, thioethers,disulfides, esters, amides, carbonates, carbamates, and so forth.Preferred linkers range in length from 5 to 40 bonds and may bebranched, straight-chain, or contain rings. Linkers may in some casesinclude double bonds. They may be hydrophobic or hydrophilic as sodesired according to the particular requirements.

It should further be understood that the connection between the L₁ groupand the detectable element, D, may be any suitable chemical connection,as would be understood by the skilled artisan. For example, the instantcompounds may in some cases be conveniently prepared by including in thedelectable element precursor a moiety that is reactive with a particularchemical group, such as, for example, an amino group, a thiol group, orthe like. The detectable element can in such a situation be readilyattached to the targeting element through the reaction of this group onthe targeting element. These types of attachments are thus understood tobe within the scope of the disclosed compounds, even if the structuraldetails of the connection are not explicitly shown.

The AA₁ group of the instant compounds may be any natural or unnaturalamino acid side chain as would be understood by the skilled artisan. Inpreferred embodiments, the AA₁ group is an aralkyl amino acid side chainthat is optionally substituted with 1 to 3 A groups. In even morepreferred embodiments, the AA₁ group is a phenylalanine side chain.

In preferred compounds, the U group is O.

The detectable element of the instant compounds is in specificembodiments a fluorescent label, a radiolabel, a chelator, or the like.Examples of radiolabels and chelators suitable for use in thesecompounds are described in PCT International Publication No.2009/124265.

In preferred embodiments of the instant compounds, the detectableelement is a fluorescent label. As is known by those of ordinary skillin the art, fluorescent labels emit electromagnetic radiation,preferably visible light, when stimulated by the absorption of incidentelectromagnetic radiation. A wide variety of fluorescent labels,including labels having reactive moieties useful for coupling the labelto reactive groups such as, for example amino groups, thiol groups, andthe like, are commercially available. See, e.g., The Molecular Probes®Handbook—A Guide to Fluorescent Probes and Labeling Technologies.

An example of a fluorescent label is fluorescein, which is widely usedin immunofluorescence labeling. Fluorescein is a xanthene dye with anabsorption maximum at 495 nanometers. A related fluorophore is OregonGreen, a fluorinated derivative of fluorescein.

The fluorescent label used in the detectable element of the compounds ofthe instant invention may in some embodiments be a pH-dependentfluorophore. Such fluorescent labels, for example as used in thecompounds labeled “LES12” and “LES13”, shown below, display afluorescence spectrum that depends on the pH of the label's environment,as would be understood by the skilled artisan, and may therefore beuseful in reporting information about the environment of the labelfollowing reaction, for example information about the location of ortype of protease labeled by the reactive compound. The pH-dependentfluorescence of various labels usefully included in the detectableelement of the instant compounds is well known. See, e.g., The MolecularProbes® Handbook—A Guide to Fluorescent Probes and LabelingTechnologies, which is hereby incorporated by reference in its entirety.

Other exemplary fluorescent labels suitable for use in the instantcompounds are bora-diaza-indecene, rhodamine, and cyanine dyes. Inparticular, bora-diaza-indecene dyes are represented by4,4-difluoro-4-bora-3a,4a-diaza-s-indacene, known as the BODIPY® dyes.Various derivatives of these dyes are known and are considered suitablefor use as a detectable element in the compounds of the instantdisclosure. See, e.g., Chen et al. (2000) J. Org. Chem. 65:2900-2906.

Another class of fluorescent label usefully employed in the compounds ofthe instant invention are the IRDye infrared dyes available from Li-Cor(www.licor.com). Non-limiting examples of these dyes are IRDye 800CW,IRDye 680RD, IRDye 680LT, IRDye 750, IRDye 700DX, IRDye 800R5, and IRDye650.

Rhodamine dyes are a class of dyes based on the rhodamine ringstructure. Rhodamines include, inter alia, tetramethylrhodamine (TMR), avery common fluorophore for preparing protein conjugates, especiallyantibody and avidin conjugates, and carboxy tetramethyl-rhodamine(TAMRA), a dye commonly used for oligonucleotide labeling and automatednucleic acid sequencing. Rhodamines are established as naturalsupplements to fluorescein-based fluorophores, which offer longerwavelength emission maxima and thus open opportunities for multicolorlabeling or staining.

Also included within the group of rhodamine dyes are the sulfonatedrhodamine series of fluorophores known as Alexa Fluor dyes. The dramaticadvances in modern fluorophore technology are exemplified by the AlexaFluor dyes, which were introduced by Molecular Probes. These sulfonatedrhodamine derivatives exhibit higher quantum yields for more intensefluorescence emission than spectrally similar probes, and have severaladditional improved features, including enhanced photostability,absorption spectra matched to common laser lines, pH insensitivity, anda high degree of water solubility.

The cyanine dyes correspond to a family of related dyes, Cy2, Cy3, Cy5,Cy7, and their derivatives, that are based on the partially saturatedindole nitrogen heterocyclic nucleus with two aromatic units beingconnected via a polyalkene bridge of varying carbon number. These probesexhibit fluorescence excitation and emission profiles that are similarto many of the traditional dyes, such as fluorescein andtetramethylrhodamine, but with enhanced water solubility,photostability, and higher quantum yields. Most of the cyanine dyes aremore environmentally stable than their traditional counterparts,rendering their fluorescence emission intensity less sensitive to pH andorganic mounting media. In a manner similar to the Alexa Fluors, theexcitation wavelengths of the Cy series of synthetic dyes are tunedspecifically for use with common laser and arc-discharge sources, andthe fluorescence emission can be detected with traditional filtercombinations. The cyanine dyes are readily available as reactive dyes orfluorophores. The cyanine dyes generally have broader absorption spectrathan members of the Alexa Fluor family, making them somewhat moreversatile in the choice of laser excitation sources for confocalmicroscopy.

In preferred embodiments, the detectable element of the instantcompounds is the cyanine dye, Cy5.

In some embodiments, it may be beneficial to include multiplefluorescent labels, radiolabels, chelators, or the like, within thedetectable element of the compounds of the invention. For example, theexemplary compounds labeled “LES12” and “LES13” below include twodifferent fluorescent labels within a single detectable element. Suchmultiple labeling can be achieved using routine coupling chemistry aswould be understood by the skilled artisan. For example, the fluorescentlabels in the “LES12” and “LES13” compounds were coupled using “click”chemistry. An example of an intermediate compound useful in thesynthesis of compounds containing multiple labels within the detectableelement by “click” chemistry is shown below (“WL938”). This compoundcontains an azido group and can thus be readily reacted with a suitablealkyne-containing reagent in a “click” reaction. The positions of thealkyne and azido groups could also be reversed, if desired, as would beunderstood by those of ordinary skill in the art.

In some embodiments, the compound of the invention is a compound offormula (I), wherein T is a peptidic targeting element, and the compoundis further described in the following numbered sentences:

1. A compound of formula (I), wherein D-T- is a short detectablepeptidic group; and

L is an ether-linked leaving element.

2. The compound of sentence 1, wherein the detectable peptidic groupcontains 1 to 4 amino acid residues.

3. The compound of sentence 2, wherein D-T is:

wherein

each AA₁, AA₂, AA₃, and AA₄ is independently an amino acid side chain or-L₁-D;

each RA is independently hydrogen or R₁;

R_(B) is hydrogen, R₁, —C(O)R₁, —C(O)OR₁, —C(O)SR₁, or—C(O)N(R₁)(R_(A));

R₁ is alkyl, alkenyl, alkynyl, aryl, aralkyl, heteroaryl, heteroaralkyl,cycloalkyl, cycloalkenyl, cycloalkylalkyl, heterocyclyl,heterocyclylalkyl, a protecting group, or -L₁-D, and is optionallysubstituted with 1 to 3 A groups;

each A is independently alkyl, alkenyl, alkynyl, alkoxy, alkanoyl,alkylamino, aryl, aryloxy, arylamino, aralkyl, aralkoxy, aralkanoyl,aralkamino, heteroaryl, heteroaryloxy, heteroarylamino, heteroaralkyl,heteroaralkoxy, heteroaralkanoyl, heteroaralkamino, cycloalkyl,cycloalkenyl, cycloalkylalkyl, cycloalkoxy, cycloalkanoyl,cycloalkamino, heterocyclyl, heterocyclyloxy, heterocyclylamino,heterocyclylalkyl, heterocyclylalkoxy, heterocyclylalkanoyl,heterocyclylalkamino, hydroxyl, thio, amino, alkanoylamino, aroylamino,aralkanoylamino, alkylcarboxy, carbonate, carbamate, guanidinyl, urea,halo, trihalomethyl, cyano, nitro, phosphoryl, sulfonyl, sulfonamido, orazido; and

L₁ is a linker.

4. The compound of sentence 3, wherein

each R_(A) is hydrogen; and

R_(B) is —C(O)OR₁.

5. The compound of sentence 3, wherein D-T- is

each AA₁ and AA₂ is independently an amino acid side chain or -L₁-D; and

each R_(A) is hydrogen.

6. The compound of sentence 3, wherein D-T- is

each AA₁, AA₂, and AA₃ is independently an amino acid side chain or-L₁-D; and

each R_(A) is hydrogen.

7. The compound of sentence 3, wherein D-T is

each AA₁, AA₂, AA₃, and AA₄ is independently an amino acid side chain or-L₁-D; and

each R_(A) is hydrogen.

8. The compound of sentence 3, wherein Li is an optionally substitutedalkyl linker, wherein each carbon atom is optionally replaced with aheteroatom.

9. The compound of sentence 3, wherein R_(B) is —C(O)OR₁.

10. The compound of sentence 3, wherein D is a fluorescent label, aradiolabel, or a chelator.

11. The compound of sentence 10, wherein D is a fluorescent label.

12. The compound of sentence 11, wherein the fluorescent label is afluorescein, an Oregon green, a bora-diaza-indecene, a rhodamine, or acyanine label.

13. The compound of sentence 12, wherein the fluorescent label is acyanine label.

14. The compound of sentence 13, wherein the cyanine label is Cy5.

The AA₁, AA₂, AA₃, and AA₄ groups in these embodiments of the instantcompounds may be independently any natural or unnatural amino acid sidechain as would be understood by the skilled artisan, or the group“-L₁-D”. In preferred embodiments, the group is an aralkyl amino acidside chain that is optionally substituted with 1 to 3 A groups. In evenmore preferred embodiments, the group is a side chain fromphenylalanine. In other preferred embodiments, the group is a side chainfrom an acidic amino acid residue, such as a side chain from an asparticacid or glutamic acid residue, or a side chain from an alkyl amino acidresidue, such as an alanine, leucine, isoleucine, valine, or other suchamino acid residue, in any combination. Side chains from other aminoacid residues, such as lysine, arginine, tyrosine, glutamine,asparagine, and the like, are also preferred in the instant compounds.

In compound embodiments where the AA₁, AA₂, AA₃, or AA₄ group is an“-L₁-D” group, the L₁ linker component may be provided by an amino acidside chain. For example, a lysine residue conveniently provides anamino-alkyl group for reaction with a suitably activated detectableelement.

A “short” detectable peptidic group is defined herein as a detectablepeptidic group having up to 10 amino acid residues.

The ether-linked leaving element, L, of the instant compounds influencesthe reactivity of the compounds with their target enzyme active site andmay also affect the specificity of targeting to a particular enzyme. Theether linkage of the leaving element in these compounds is in contrastto the ester linkage of other activity based probes, such as theacyloxymethyl ketones (AOMKs). An ether-linked leaving element, such as,for example, a phenol ether-linked leaving element, may provide improvedstability in vivo over ester-linked or other types of probes.

In some embodiments, the ether-linked leaving element of the instantcompounds comprises a quencher. The term “quencher” refers to a chemicalentity that modulates the emission of a fluorophore. In some cases, aquencher may itself be a fluorescent molecule that emits fluorescence ata characteristic wavelength distinct from the label whose fluorescenceit is quenching. Thus, a fluorophore may act as a quencher whenappropriately coupled to another dye and vice versa. In thesesituations, the increase in fluorescence from the acceptor molecule,which is of a different wavelength to that of the donor label, mayseparately report interactions of the labeled compound with itsenvironment, such as, for example, the active site of a target enzyme.In some cases, the quencher does not itself fluoresce (i.e., thequencher is a “dark acceptor”). Such quenchers include, for example,dabcyl, methyl red, the QSY diarylrhodamine dyes, and the like. Inparticular, dabcyl (4-dimethylamino-phenylazo)benzoic acid) is a commondark quencher used widely in many assays, such as “molecular beacons”for DNA detection. U.S. Pat. No. 5,989,823. Diazo dyes of the BHQseries, which are referred to as “Black Hole Quenchers”, provide a broadrange of absorption which overlaps well with the emission of manyfluorophores. PCT International Publication No. WO01/86001. The QSYseries dyes from Molecular Probes is another example of dark quencherdyes that have been used extensively as quenching reagents in manybioassays. U.S. Pat. No. 6,399,392.

QSY 7 in particular is a nonfluorescent diarylrhodamine derivative. U.S.Patent Application Publication No. 2005/0014160. QSY21 is anonfluorescent diarylrhodamine chromophore with strong absorption in thevisible spectrum, and is an effective fluorescence quencher.Fluorophore/quencher pairs are further illustrated in U.S. PatentApplication Publication No. 2004/0241679.

IRDye QC-1 (available from Li-Cor) is another example of anon-fluorescent dye that is suitable for use as a quencher in theinstant compounds. It efficiently quenches fluorescence from a widerange of fluorophores, including those ranging in wavelength from thevisible region to the near-infrared.

In some embodiments of the instant compounds, the leaving group element,L, is L₂-L₃-Q, wherein L₂ is a phenoxy group, L₃ is a linker, and Q is aquencher. The leaving group element may be, for example,

wherein each Y is independently an electron-withdrawing group orhydrogen. In such compounds, each Y may independently be a halogen orhydrogen. In specific compounds, the L group is, for example,

The L₃ linker group of the above-described leaving element may be anysuitable linker, as would be understood by the person of ordinary skillin the art. In particular, the L₃ linker group may be, for example, anL₁ group, as described above.

In other specific compounds, the L group is, for example,

wherein R is a QSY quencher and n is an integer from 1 to 8. In specificembodiments, the QSY quencher is a hydrophilic quencher, such as, forexample, a sulfo-QSY quencher.

In some specific embodiments, the compounds of the instant disclosurehave the structure of formula (II):

In some more specific embodiments, the compounds of the instantdisclosure have the structure of formula (III):

In these embodiments, m and n are independently integers from 1 to 16.

In some embodiments, R is QSY21 or sulfo-QSY21, and D is Cy5.

Specific non-limiting compound embodiments of the invention include:

where R=QSY21 and n=6;

R=Sulfo-QSY21 and n=6;

R=QSY21 and n=2; and

R=Sulfo-QSY21 and n=2.

In some embodiments, the compound of the invention is a compound havingthe structure of formula (IV):

wherein T is a peptidic targeting element, and the compound is furtherdescribed in the following numbered sentences:

1. A compound of formula (IV), wherein D-T- is a short detectablepeptidic group;

L₃ is a linker; and

Q is a quencher. 2. The compound of sentence 1, wherein the detectablepeptidic group contains 1 to 4 amino acid residues.

3. The compound of sentence 2, wherein D-T is:

wherein

each AA₁, AA₂, AA₃, and AA₄ is independently an amino acid side chain or-L₁-D;

each R_(A) is independently hydrogen or R₁;

R_(B) is hydrogen, R₁, —C(O)R₁, —C(O)OR₁, —C(O)SR₁, or—C(O)N(R₁)(R_(A));

R₁ is alkyl, alkenyl, alkynyl, aryl, aralkyl, heteroaryl, heteroaralkyl,cycloalkyl, cycloalkenyl, cycloalkylalkyl, heterocyclyl,heterocyclylalkyl, a protecting group, or -L₁-D, and is optionallysubstituted with 1 to 3 A groups;

each A is independently alkyl, alkenyl, alkynyl, alkoxy, alkanoyl,alkylamino, aryl, aryloxy, arylamino, aralkyl, aralkoxy, aralkanoyl,aralkamino, heteroaryl, heteroaryloxy, heteroarylamino, heteroaralkyl,heteroaralkoxy, heteroaralkanoyl, heteroaralkamino, cycloalkyl,cycloalkenyl, cycloalkylalkyl, cycloalkoxy, cycloalkanoyl,cycloalkamino, heterocyclyl, heterocyclyloxy, heterocyclylamino,heterocyclylalkyl, heterocyclylalkoxy, heterocyclylalkanoyl,heterocyclylalkamino, hydroxyl, thio, amino, alkanoylamino, aroylamino,aralkanoylamino, alkylcarboxy, carbonate, carbamate, guanidinyl, urea,halo, trihalomethyl, cyano, nitro, phosphoryl, sulfonyl, sulfonamido, orazido; and

L₁ is a linker.

4. The compound of sentence 3, wherein

each R^(A) is hydrogen; and

R_(B) is —C(O )OR₁.

5. The compound of sentence 3, wherein D-T- is

each AA₁ and AA₂ is independently an amino acid side chain or -L₁-D; and

each R_(A) is hydrogen.

6. The compound of sentence 3, wherein D-T- is

each AA₁, AA₂, and AA₃ is independently an amino acid side chain or-L₁-D; and

each R^(A) is hydrogen.

7. The compound of sentence 3, wherein D-T is

each AA₁, AA₂, and AA₃ and AA4 is independently an amino acid side chainor -L₁-D; and each R_(A) is hydrogen.

8. The compound of sentence 3, wherein L₁ is an optionally substitutedalkyl linker, wherein each carbon atom is optionally replaced with aheteroatom.

9. The compound of sentence 3, wherein R_(B) is —C(O)OR₁.

10. The compound of sentence 3, wherein D is a fluorescent label, aradiolabel, or a chelator.

11. The compound of sentence 10, wherein D is a fluorescent label.

12. The compound of sentence 11, wherein the fluorescent label is afluorescein, an Oregon green, a bora-diaza-indecene, a rhodamine, or acyanine label.

13. The compound of sentence 12, wherein the fluorescent label is acyanine label.

14. The compound of sentence 13, wherein the cyanine label is Cy5.

The AA₁, AA₂, AA₃, and AA₄ groups in these embodiments of the instantcompounds may be independently any natural or unnatural amino acid sidechain as would be understood by the skilled artisan, or the group“-L₁-D”. In preferred embodiments, the group is an aralkyl amino acidside chain that is optionally substituted with 1 to 3 A groups. In evenmore preferred embodiments, the group is a side chain fromphenylalanine. In other preferred embodiments, the group is a side chainfrom an acidic amino acid residue, such as a side chain from an asparticacid or glutamic acid residue, or a side chain from an alkyl amino acidresidue, such as an alanine, leucine, isoleucine, valine, or other suchamino acid residue, in any combination. Side chains from other aminoacid residues, such as lysine, arginine, tyrosine, glutamine,asparagine, and the like, are also preferred in the instant compounds.

In compound embodiments where the AA₁, AA₂, AA₃, and AA₄ group is an“-L₁-D” group, the L₁ linker component may be provided by an amino acidside chain. For example, a lysine residue conveniently provides anamino-alkyl group for reaction with a suitably activated detectableelement.

A “short” detectable peptidic group is defined herein as a detectablepeptidic group having up to 10 amino acid residues.

Other specific non-limiting compound embodiments of the inventioninclude:

Pharmaceutical Compositions

In another aspect, the instant invention provides pharmaceuticalcompositions comprising a compound of the invention and apharmaceutically acceptable carrier. Such compositions are useful, forexample, in the imaging of tissues in an animal and are further usefulin assessing the activity of enzymes in the animal, for example,protease enzymes. In particular, for compounds of the invention thatlabel cathepsins, the pharmaceutical compositions may usefully serve astools for the non-invasive optical imaging of cancer cells.

Pharmaceutically acceptable carriers are well known in the art andinclude, for example, aqueous solutions such as water or physiologicallybuffered saline or other solvents or vehicles such as glycols, glycerol,oils such as olive oil or injectable organic esters. In a specificembodiment, when such pharmaceutical compositions are for humanadministration, the aqueous solution is pyrogen free, or substantiallypyrogen free. The excipients may be chosen, for example, to effectdelayed release of an agent or to selectively target one or more cells,tissues or organs. The pharmaceutical composition may be in dosage unitform such as tablet, capsule, sprinkle capsule, granule, powder, syrup,suppository, injection or the like. The composition may also be presentin a transdermal delivery system, e.g., a skin patch.

A pharmaceutically acceptable carrier may contain physiologicallyacceptable agents that act, for example, to stabilize or to increase theabsorption of a compound of the instant invention. Such physiologicallyacceptable agents include, for example, carbohydrates, such as glucose,sucrose or dextrans, antioxidants, such as ascorbic acid or glutathione,chelating agents, low molecular weight proteins or other stabilizers orexcipients. The choice of a pharmaceutically acceptable carrier,including a physiologically acceptable agent, depends, for example, onthe route of administration of the composition. The pharmaceuticalcomposition also may comprise a liposome or other polymer matrix, whichmay have incorporated therein, for example, a compound of the invention.Liposomes, for example, which consist of phospholipids or other lipids,are nontoxic, physiologically acceptable and metabolizable carriers thatare relatively simple to make and administer.

The phrase “pharmaceutically acceptable” is employed herein to refer tothose compounds, materials, compositions, and/or dosage forms that are,within the scope of sound medical judgment, suitable for use in contactwith the tissues of human beings and animals without excessive toxicity,irritation, allergic response, or other problem or complication,commensurate with a reasonable benefit/risk ratio.

The phrase “pharmaceutically acceptable carrier” as used herein means apharmaceutically acceptable material, composition, or vehicle, such as aliquid or solid filler, diluent, excipient, solvent, or encapsulatingmaterial, involved in carrying or transporting the subject compoundsfrom one organ, or portion of the body, to another organ, or portion ofthe body. Each carrier must be “acceptable” in the sense of beingcompatible with the other ingredients of the formulation and notinjurious to the patient. Some examples of materials that can serve aspharmaceutically acceptable carriers include: (1) sugars, such aslactose, glucose and sucrose; (2) starches, such as corn starch andpotato starch; (3) cellulose, and its derivatives, such as sodiumcarboxymethyl cellulose, ethyl cellulose and cellulose acetate; (4)powdered tragacanth; (5) malt; (6) gelatin; (7) talc; (8) excipients,such as cocoa butter and suppository waxes; (9) oils, such as peanutoil, cottonseed oil, safflower oil, sesame oil, olive oil, corn oil andsoybean oil; (10) glycols, such as propylene glycol; (11) polyols, suchas glycerin, sorbitol, mannitol and polyethylene glycol; (12) esters,such as ethyl oleate and ethyl laurate; (13) agar; (14) bufferingagents, such as magnesium hydroxide and aluminum hydroxide; (15) alginicacid; (16) pyrogen-free water; (17) isotonic saline; (18) Ringer'ssolution; (19) ethyl alcohol; (20) phosphate buffer solutions; and (21)other non-toxic compatible substances employed in pharmaceuticalformulations. See Remington: The Science and Practice of Pharmacy, 20thed. (Alfonso R. Gennaro ed.), 2000.

A pharmaceutical composition containing a compound of the instantinvention may be administered to a subject by any of a number of routesof administration including, for example, orally (for example, drenchesas in aqueous or non-aqueous solutions or suspensions, tablets, boluses,powders, granules, pastes for application to the tongue); sublingually;anally, rectally, or vaginally (for example, as a pessary, cream, orfoam); parenterally (including intramuscularly, intravenously,subcutaneously, or intrathecally as, for example, a sterile solution orsuspension); nasally; intraperitoneally; subcutaneously; transdermally(for example as a patch applied to the skin); or topically (for example,as a cream, ointment or spray applied to the skin). The compound mayalso be formulated for inhalation. In certain embodiments, a compound ofthe instant invention may be simply dissolved or suspended in sterilewater. Details of appropriate routes of administration and compositionssuitable for same can be found in, for example, U.S. Pat. Nos.6,110,973; 5,763,493; 5,731,000; 5,541,231; 5,427,798; 5,358,970; and4,172,896, as well as in patents cited therein.

Methods of Labeling and Visualizing

In another aspect, the invention provides methods of visualizing a tumorin an animal, comprising the step of administering a composition of theinvention to the animal.

In yet another aspect, the invention provides methods of visualizing atumor in an animal, comprising the steps of administering a compositionof the invention to the animal, and measuring a detectable signalgenerated in the animal from a reaction of the composition with acathepsin cysteine protease, wherein the detectable signal is associatedwith a tumor in the animal.

In some embodiments of the methods, the detectable signal is afluorescent signal. In some embodiments, the fluorescent signal isgenerated at a tumor margin.

The administration of peptide imaging agents to an animal is wellunderstood by those of ordinary skill in the art. In preferredembodiments, the agent is administered by injection, although any othersuitable means of administration is considered within the scope of theinvention.

The methods of the invention are directed at the labeling andvisualization of a protease, in particular a cysteine protease, in ananimal. Suitable animals include animals expressing cysteine proteases,particularly in tumor cells. In preferred embodiments, the animal is amammal. In highly preferred embodiments, the animal is a human. In otherpreferred embodiments, the animal is a livestock animal or a pet.

In some embodiments, the methods of the invention comprise the step ofmeasuring a detectable signal generated in the animal. Methods ofmeasuring the detectable signal include, but are not limited to, imagingmethods, for example fluorescent imaging methods. In some embodiments,the fluorescent imaging system is, for example, a Xenogen IVIS 100system, but any suitable imaging system may be used.

It will be readily apparent to one of ordinary skill in the relevantarts that other suitable modifications and adaptations to the methodsand applications described herein may be made without departing from thescope of the invention or any embodiment thereof. Having now describedthe present invention in detail, the same will be more clearlyunderstood by reference to the following Example, which is includedherewith for purposes of illustration only and is not intended to belimiting of the invention.

EXAMPLE Synthesis and Characterization of Quenched Fluorescent CysteineCathepsin Imaging Probes Containing a Novel Phenoxymethyl Ketone (PMK)Electrophile

The goal of this work was to develop a qABP with overall improved invivo properties compared to the existing qABPs that could be used fornon-invasive optical imaging of cancer. It was therefore decided tooptimize three major elements of the probe, the quencher, the linker andthe electrophilic “warhead”. One of the biggest drawbacks of thecysteine cathepsin qABPs reported to date is the relatively poor aqueoussolubility. Sulfonate groups were therefore introduced to the QSY21quencher (Xing et al. (2005) J. Am. Chem. Soc. 127:4158-9) in order toimprove the water solubility and thereby the bio-distribution of theprobe. The length of the spacer tethering the electrophile and thequencher was also varied in order to decrease the lipophilicity of theqABP. Finally, a new electrophile was explored in order to increase therange of possible cathepsin targets. Since several members of thecysteine cathepsin family are upregulated in a variety of cancers(Mohamed & Sloane (2006) Nat. Rev. Cancer (2006) 6:764-75), a brighterfluorescence signal in tumors would be expected if the probe targets abroad spectrum of cysteine cathepsin activities. In order to obtain amore pan-reactive probe, the size of the electrophile was decreased, andthe reactivity was increased. It has previously been shown that the2,3,5,6-tetrafluoro substituted phenoxymethyl ketone (PMK) electrophilehas a greater reactivity for cysteine dipeptidyl aminopeptidasescompared to the 2,6-dimethylbenzoic acid derived acyloxymethyl ketone(AOMK). Deu et al. (2010) Chem Biol. 17:808-819. The smaller size of thePMK could also increase the pan-reactivity since the binding grooves ofsome of the cysteine cathepsins, are sterically restricted. Blum et al.(2005) Nat. Chem. Biol. 1:203-9; Blum et al. (2007) Nat. Chem. Biol.3:668-77; Paulick & Bogyo (2011) ACS Chem. Biol. 6:563-72. Furthermore,the phenol ether is expected to be more stable in vivo compared to theAOMK electrophile which contains an ester linkage that can be degradedby estereases.

As a starting point for this study 7 analogs (2-8) of qABP GB137 (1)were synthesized. Blum et al. (2007) Nat. Chem. Biol. 3:668-77. (FIG. 1a) These compounds represent all combinations of the two electrophiles,two quenchers and two linker lengths. All probes were synthesized usingan optimized, solution chemistry based procedure as described in thedescription associated with Scheme 1 below. The specificity and potencyof the probe were initially tested by labeling intact RAW 264.7 cells(Mouse leukaemic monocyte macrophage cell line) (FIG. 1b ). Severaltrends were observed in the properties of the probes. All of the theSulfo-QSY21 functionalized qABPs (2, 4, 6 and 8) showed stronger overallcathepsin labeling compared to the more hydrophobic QSY21 containingprobes (1, 3, 5 and 7). Interestingly, the change in the spacer lengthfrom a hexyl to an ethyl linker did not have a dramatic influence on thelabeling profile. Perhaps the most striking observation was that theqABPs with the PMK electrophile showed a broader cysteine cathepsinlabeling profile compared to their AOMK counterparts. Probes 5-8 showedrobust cathepsin X labeling and Sulfo-QSY21 functionalized probes 6 and8 were able to label a higher molecular weight pro-form of cathepsin L.The identities of the fluorescently labeled cathep sins were determinedby immunoprecipitation (FIG. 4a ). Upon performing titration labelingexperiments in live RAW cells, several other interesting trends wereobserved (FIG. 1c,d . FIG. 4b,c ). The most hydrophobic qABPs (1 and 5)reach a reduced maximum of labeling intensity at 0.5 μM, suggesting thattheir reduced water solubility results in precipitation of the probes atthe higher concentrations. The shorter spacer length seems to bebeneficial, with all probes carrying the ethyl spacer giving brighterlabeling compared to their hexyl containing counterparts. When comparingthe AOMKs with the PMKs, a clear difference in selectivity is observed.The AOMK qABPs preferentially label cathepsins S and L and only athigher concentrations label cathepsin B. Surprisingly, the AOMK qABPs2-4 label cathepsin X, even though prior studies had shown that severalother related AOMKs are incapable of labeling this target (Paulick &Bogyo (2011) ACS Chem. Biol. 6:563-72). The PMK qABPs also labeled alltarget cysteine cathepsins with equal intensity, even at the lower probeconcentrations. Together, these experiments demonstrate that increasedhydrophilicity improves labeling intensity and that the novel PMK qABPshave a broader, more pan-cysteine cathepsin labeling profile.

Because the PMK qABP 8 was the most optimal in terms of overall labelingintensity and broad cathepsin reactivity, it was decided to proceed withthis probe for further in vivo studies. To further define the targetselectivity, RAW cell lysates were labeled with increasingconcentrations of qABP 8 at pH 5.5. These results demonstrated that theprobe is most potent towards cathepsins B and X with labeling observedat concentrations as low as 5 nM. However, labeling of all of thecathepsins (B,S, L, X) was saturated by 500 nM of the probe (FIG. 2a ).When the probe was used for a timecourse labeling of live RAW cells atthe set concentration of 500 nM, a rapid saturation of cathepsin X wasobserved, and then a more slow labeling of cathepsin S, L and B withcathepsin B labeling signal increasing even at 120 min (FIG. 2b ). Thesedata indicate that the probe is likely able to access pools of cathepsinX most rapidly, perhaps due to its localization within or on the surfaceof the cells. It also indicates that cathepsins B and X may be inalternate locations in the cells which can be accessed by the probe todifferent extents. In order to test the stability of the new PMK probe,the effects of serum exposure on labeling in RAW cells were examined(FIG. 1c ). Whereas 4 hours of serum pre-exposure to the original AOMKprobe 1 resulted in a loss of nearly 70% of target labeling, more than80% of the labeling was retained for PMK qABP 8. Pre-treatment of thecells with the cysteine cathepsin inhibitor JPM-OEt also blocked morethan 90% of this labeling. Given the stability and improved labelingproperties of the PMK probe, live cell fluorescence microscopy studieswere next performed. These results confirmed that the probe producedbright and specific labeling signals and that the majority of the probelabeled cathepsins reside in lysosomes (FIG. 2d ).

Given the positive live cell labeling propertied of the new PMKelectrophile, the best performing PMK qABPs 2, 6 and 8 were tested in anorthotopic mouse model of breast cancer. Tao et al. (2008) BMC Cancer8:228. In addition these PMK probes were compared to the original AOMKprobe 1 (FIG. 3 and FIG. 5). 4T1 cells were implanted in the number 2and 7 mammary fat pads of Balb/c mice, and tumor growth was monitored.When tumors were established, the mice were injected with equimolaramounts of qABPs (20 nmol) via tail vein, and the Cy5 fluorescence wasnoninvasively imaged over time (FIG. 3a,b ). Again, these resultsconfirmed that the qABP 8 proved to be superior. Robust tumor-specificactivation of fluorescence could be observed for probe 8 specifically inthe tumor region with high overall contrast. This signal continued toincrease over time up to the end of the time course. Ultimately probe 8achieved a more than twenty fold enhanced tumor specific fluorescencesignal compared to probe 1. Good tumor specific contrast was alsoobserved for probe 6 and to a lesser extent for probe 2, although bothstill outcompeted probe 1 by more than tenfold (FIG. 5a,b ). After thecompletion of the time course, the tumors were excised and tumorfluorescence was measured ex vivo, followed by homogenization andanalysis of the fluorescently labeled proteins by SDS-PAGE

(FIG. 3c and FIG. 5c ). The quantification of the ex vivo fluorescenceand the total cysteine cathepsin labeling showed a similar trend as seenin the noninvasive optical imaging studies (FIG. 3d and FIG. 5d ). Todetermine the cellular source of the probe fluorescence,immuno-fluorescence staining of tumor tissue sections from probe labeledmice were stained using the macrophage marker CD68 (FIG. 3e and FIG. 5e). Cy5 fluorescence localized to CD68 positive cells, however, not allCD68 positive cells were also probe 8 positive, indicating differentactivation states of the tumor-associated macrophages. More detailedanalysis with confocal laser scanning microscopy (CLSM) confirmed thatall cells that were positive for probe 8 were CD68 positive, but thatprobe labeled cathepsins and the CD68 signals do not co-localize to thesame vesicles (FIG. 3f and FIG. 5f ). Taken together, these data confirmthat increasing the hydrophilicity of the quencher, shortening of thespacer and the introduction of a more reactive and sterically lessrestricted nucleophilic trap resulted in a qABP with a broad cysteinecathepsin reactivity and overall improved in vivo properties.

Although very distinct functions have been described for some of thecysteine cathepsin family members, (Conus & Simon (2010) Swiss Med.Wkly. 140:w13042) other roles are redundant and alterations in theactivity of one cathepsin can influence the activity of others. Forexample, loss of cathepsin B is compensated by increased activity ofcathepsin X (Sevenich et al. (2010) Proc. Natl Acad. Sci. USA107:2497-502) and upregulation of cathepsin B results in downregulationof cathepsin L (Gopinathan et al. (2012) Gut 61:877-84). Therefore abroad spectrum probe is highly valuable as it facilitates the readout ofmultiple cysteine cathepsins in one experiment and enables thecomparison of the activities of the individual cathepsins with respectto one another. The usefulness of such pan-reactive ABPs has beendemonstrated by the pan-serine hydrolase fluorophosphonate probes (Liuet al. (1999) Proc. Natl Acad. Sci. USA 96:14694-9) and the pan-reactiveproteasome probe MV151 (Verdoes et al. (2006) Chem. Biol. 13:1217-26).Furthermore, because the PMK-based qABPs are highly reactive towardscathepsin X these scaffolds can be used to generate selective qABPsagainst this still poorly understood cysteine cathepsin. (Paulick &Bogyo (2011) ACS Chem. Biol. 6:563-72).

In conclusion, a novel class of quenched fluorescent activity-basedprobes have been synthesized bearing a PMK electrophile with greaterreactivity and broader selectivity compared to the previously reportedAOMK based probes. The hydrophilicity of the qABP has furthermore beenincreased by introducing a sulfonated quencher and shortening the spacertethering the electrophile and the quencher, resulting in greateraqueous solubility and improved in vivo properties resulting in enhancedcontrast in noninvasive optical imaging of cancer.

METHODS General

All resins and reagents were purchased from commercial suppliers andused without further purifications. All solvents used were HPLC grade.All water-sensitive reactions were performed in anhydrous solvents underpositive pressure of argon. Reactions were analyzed by LC-MS using anAPI 150EX single-quadrupole mass spectrometer (Applied Biosystems).Reverse-phase HPLC was conducted with an AKTA explorer 100 (AmershamPharmacia Biotech) using C18 columns. NMR spectra were recorded on aVarian 400 MHz (400/100), Varian 500 MHz (500/125) or a Varian Inova 600MHz (600/150 MHz) equipped with a pulsed field gradient accessory.Chemical shifts are given in ppm (δ) relative to tetramethylsilane as aninternal standard. Coupling constants are given in Hz. Fluorescent gelswere scanned using a Typhoon 9400 flatbed laser scanner (GE Healthcare).In-gel labeling intensities were quantified using Image J software.Statistical analysis was performed using Microsoft Excel, and s.e.m. wascalculated by dividing the s.d. by the square root of n. Fluorescentmicroscopy images were acquired on a Zeiss confocal LSM 710 and a ZeissAxiovert 200 M inverted microscope equipped with a 10×, 40× and 63×objective (Carl Zeiss). Slidebook software was used to control themicroscope and camera and for data analysis (Intelligent ImagingInnovations).

qABP Synthesis

The synthetic scheme for synthesis of the following compounds isdepicted below in Scheme 1.

2,6-dimethyl-4-((6-(tritylamino)hexyl)carbamoyl)benzoic acid (11a).Mono-trityl 1,6-diaminohexane acetic acid salt (9a) (117.2 mg, 0.28mmol) was taken up in DCM and washed with sat. aq. NaHCO₃, dried overNa₂SO₄ and concentrated in vacuo. The amine was dissolved in DMF andHOBt monohydrate (43 mg, 0.28 mmol, 1 equiv.), EDC (54 mg, 0.28 mmol, 1equiv.) and 2,6-dimethylterephthalic acid (10) (54.4 mg, 0.28 mmol, 1equiv.) were added and the reaction mixture was stirred overnight,before being concentrated in vacuo. The crude was purified by flashcolumn chromatography (DCM→5% MeOH in DCM) and subsequently taken up inDCM and washed with water and dried over MgSO₄ to yield 70 mg (0.13mmol, 47% isolated yield).

2,6-dimethyl-4-((2-(tritylamino)ethyl)carbamoyl)benzoic acid (11b).Mono-trityl ethylenediamine acetic acid salt (9b) (97.9 mg, 0.27 mmol)was taken up in DCM and washed with sat. aq. NaHCO₃, dried over Na₂SO₄and concentrated in vacuo. The amine was dissolved in DMF and HOBtmonohydrate (43 mg, 0.28 mmol, 1.04 equiv.), EDC (61 mg, 0.32 mmol, 1.2equiv.) and 2,6-dimethylterephthalic acid (10) (52 mg, 0.27 mmol, 1equiv.) were added and the reaction mixture was stirred overnight,before being concentrated in vacuo. The crude was purified by flashcolumn chromatography (DCM→5% MeOH in DCM) and subsequently taken up inDCM and washed with water and dried over MgSO₄ to yield 28 mg (0.06mmol, 22% isolated yield).

2,3,5,6-tetrafluoro-4-hydroxy-N-(6-(tritylamino)hexyl)benzamide (13a).Mono-trityl 1,6-diaminohexane acetic acid salt (9a) (117.2 mg, 0.28mmol) was taken up in DCM and washed with sat. aq. NaHCO3, dried overNa₂SO₄ and concentrated in vacuo. The amine was dissolved in DMF andHOBt monohydrate (43 mg, 0.28 mmol, 1 equiv.), EDC (54 mg, 0.28 mmol, 1equiv.) and 2,3,5,6-tetrafluoro-4-hydroxybenzoic acid (12) (59 mg, 0.28mmol, 1 equiv.) were added and the reaction mixture was stirredovernight, before being concentrated in vacuo. The crude was purified byflash column chromatography (15% ->30% ethyl acetate in hexane) to yield90 mg (0.16 mmol, 58% isolated yield).

2,3,5,6-tetrafluoro-4-hydroxy-N-(2-(tritylamino)ethyl)benzamide (13b).Mono-trityl ethylenediamine acetic acid salt (9b) (100 mg, 0.28 mmol)was taken up in DCM and washed with sat. aq. NaHCO3, dried over Na₂SO₄and concentrated in vacuo. The amine was dissolved in DMF and HOBtmonohydrate (43 mg, 0.28 mmol, 1 equiv.), EDC (54 mg, 0.28 mmol, 1equiv.) and 2,3,5,6-tetrafluoro-4-hydroxybenzoic acid (12) (59 mg, 0.28mmol, 1 equiv.) were added and the reaction mixture was stirredovernight, before being concentrated in vacuo. The crude was purified byflash column chromatography (20%->35% ethyl acetate in hexane) to yield90 mg (0.18 mmol, 65% isolated yield). ¹H NMR (400 MHz, DMSO) δ=8.77 (t,J=6.0, 1H), 7.39 (d, J=7.8, 6H), 7.27 (t, J=7.7 , 6H), 7.17 (t, J=7.2,3H), 3.40-3.35 (m, 2H), 2.86-2.77 (m, 1H), 2.14-2.04 (m, 2H).

Intermediate 15. Potassium fluoride (3 mg, 52 μmol, 3 equiv.) wassuspended in DMF by sonication for 5 min, after which carboxylic acid11a (10 mg, 19 μmol, 1.1 equiv.) was added. The reaction mixture wasstirred for 10 min, before chloromethyl ketone 14 (9.7 mg, 17.3 μmol, 1equiv.) was added. After 2 hr the reaction mixture was concentrated invacuo and the crude was taken up in 1% TFA in DCM and stirred for 30min, before being quenched by the addition of triisopropylsilane untilthe solution was colorless. After coevaporation with toluene (3×) thetitle compound was purified by HPLC (preparatory reverse phase C₁₈column, CH₃CN/H₂O 0.1% TFA, 15:85 to 55:45 over 20 min; 5 mL/min),followed by lyophilization to afford 15 as a white powder (3.12 mg, 3.46mol, 20% over 2 steps).

Intermediate 16. Potassium fluoride (3 mg, 52 μmol, 3 equiv.) wassuspended in DMF by sonication for 5 min, after which carboxylic acid11b (9.5 mg, 20 μmol, 1.1 equiv.) was added. The reaction mixture wasstirred for 10 min, before chloromethyl ketone 14 (10 mg, 17.9 mol, 1equiv.) was added. After 1.5 hr the reaction mixture was concentrated invacuo and the crude was taken up in 1% TFA in DCM and stirred for 30min, before being quenched by the addition of triisopropylsilane untilthe solution turned colorless. After coevaporation with toluene (3×)intermediate 16 was purified by HPLC (preparatory reverse phase C₁₈column, CH₃CN/H₂O 0.1% TFA, 15:85 to 55:45 over 20 min; 5 mL/min),followed by lyophilization to afford a white powder (3.99 mg, 4.57 mol,26% over 2 steps). ¹H NMR (500 MHz, CD₃OD) δ7.80 (s, 1H), 7.42 (s, 1H),7.35-7.18 (m, 10H), 5.06 (s, 2H), 4.85-4.78 (m, 2H), 4.42 (dd, J=13.1,6.2 Hz, 1H), 4.37 (dd, J=10.1, 4.0 Hz, 1H), 3.64 (t, J=5.7 Hz, 2H), 3.18(t, J=4.8 Hz, 2H), 3.12 (dd, J=13.7, 7.0 Hz, 1H), 3.01 (t, J=7.3 Hz,2H), 2.94 (dd, J=13.6, 8.9 Hz, 1H), 2.41 (s, 3H), 2.34 (s, 3H),1.92-1.82 (m, 1H), 1.67-1.57 (m, 1H), 1.49-1.26 (m, 4H), 1.42 (s, 9H).

Intermediate 17. Potassium fluoride (6.3 mg, 108 mol, 3 equiv.) wassuspended in DMF by sonication for 5 min, after which phenol 13a (21.5mg, 39 mol, 1.1 equiv.) was added. The reaction mixture was stirred for10 min, before chloromethyl ketone 14 (20 mg, 36 μmol, 1 equiv.) wasadded. The reaction mixture was stirred at 80° C. for 5 hr, before beingconcentrated in vacuo. The crude was taken up in 1% TFA in DCM andstirred for 30 min, before being quenched by the addition oftriisopropylsilane until the solution turned colorless. Aftercoevaporation with toluene (3×), purification by HPLC (preparatoryreverse phase C₁₈ column, CH₃CN/H₂O 0.1% TFA, 25:75 to 70:30 over 20min; 5 mL/min), followed by lyophilization afforded the title compoundas a white powder (16.6 mg, 17.5 mol, 49% over 2 steps). ¹H NMR (500MHz, CD₃OD) δ7.29 (m , 10H), 5.07 (s, 2H), 4.86 (m , 2H), 4.44 (m , 2H),3.41 (t, J=6.8, 2H), 3.10 (dd, J=13.5, 7.0, 1H), 3.02 (t, J=6.8, 2H),2.97-2.91 (m, 3H), 1.93-1.81 (m, 1H), 1.73-1.62 (m, 4H), 1.62-1.53 (m,1H), 1.51-1.46 (m, 4H), 1.43 (s, 9H), 1.45-1.25 (m, 4H).

Intermediate 18. Potassium fluoride (6.3 mg, 108 μmol, 3 equiv.) wassuspended in DMF by sonication for 5 min, after which phenol 13b (19.4mg, 39 mol, 1.1 equiv.) was added. The reaction mixture was stirred for10 min, before chloromethyl ketone 14 (20 mg, 36 μmol, 1 equiv.) wasadded. The reaction mixture was stirred at 80° C. for 3 hr, before beingconcentrated in vacuo. The crude was taken up in 1% TFA in DCM andstirred for 30 min, before being quenched by the addition oftriisopropylsilane until the solution turned colorless. Aftercoevaporation with toluene (3×), purification by HPLC (preparatoryreverse phase C₁₈ column, CH₃CN/H₂O 0.1% TFA, 20:80 to 60:40 over 20min; 5 mL/min), followed by lyophilization afforded the title compoundas a white powder (15.4 mg, 17.3 μmol, 48% over 2 steps). ¹H NMR (400MHz, CD₃OD) δ=7.36-7.12 (m, 10H), 5.05 (s, 2H), 4.86-4.81 (m, 2H),4.42-4.37 (m, 2H), 3.64 (t, J=6.5, 2H), 3.14 (t, J=6.5, 2H), 3.08 (dd,J=13.9, 7.2, 1H), 2.99 (t, J=6.5, 2H), 2.91 (dd, J=13.9, 8.4, 1H),1.90-1.78 (m, 1H), 1.62-1.48 (m, 1H), 1.41 (s, 9H), 1.46-1.20 (m, 4H).

Probe 1 (GB137). Intermediate 15 (1.5 mg, 1.7 μmol) was taken up in DMSO(50 μl) and QSY21-NHS (1.39 mg, 1.7 μmol, 1 equiv.) and DiPEA (1.5 μl,8.5 μmol, 5 equiv.) were added. After 1 hr the QSY21 amide was purifiedby HPLC (preparatory reverse phase C₁₈ column, CH₃CN/H₂O 0.1% TFA, 40:60to 80:20 over 20 min; 5 mL/min), followed by lyophilization. To removethe Boc protective group the resulting dark blue powder was taken up inTFA/DCM (1/1) and reacted for 30 min, before coevaporation with toluene(3×) to give 2.42 mg of the corresponding TFA salt (1.6 μmol, 95% over 2steps). The amine was dissolved in DMSO (50 μl) and Cy5-NHS (1.3 mg,1.76 μmol, 1.1 equiv.) and DiPEA (1.4 μl, 8 μl mol, 5 equiv.) wereadded. After 1 hr, purification by HPLC (preparatory reverse phase C₁₈column, CH₃CN/H₂O 0.1% TFA, 40:60 to 75:25 over 20 min; 5 mL/min),followed by lyophilization afforded probe 1 as a dark blue powder (2.0mg, 0.99 μmol, 62%).

Probe 2 (BMV122). Intermediate 15 (1.5 mg, 1.7 μmol) was taken up inDMSO (50 μl) and Sulfo-QSY21-NHS (1.66 mg, 1.7 μmol, 1 equiv.) and DiPEA(1.5 μl, 8.5 μmol, 5 equiv.) were added. After 1 hr the Sulfo-QSY21amide was purified by HPLC (preparatory reverse phase C₁₈ column,CH3CN/H₂O 0.1% TFA, 30:70 to 70:30 over 20 min; 5 mL/min), followed bylyophilization. To remove the Boc protective group the resulting darkblue powder was taken up in TFA/DCM (1/1) and reacted for 30 min, beforecoevaporation with toluene (3×) to give 2.29 mg of the corresponding TFAsalt (1.39 μmol, 81% over 2 steps). The amine was dissolved in DMSO (50μl) and Cy5-NHS (1.1 mg, 1.5 μmol, 1.1 equiv.) and DiPEA (1.2 μl, 7μmol, 5 equiv.) were added. After 1 hr, purification by HPLC(preparatory reverse phase C₁₈ column, CH₃CN/H₂O 0.1% TFA, 15:85 to50:50 over 20 min; 5 mL/min), followed by lyophilization afforded probe2 as a dark blue powder (1.83 mg, 0.84 μmol, 61%).

Probe 3 (BMV145) Intermediate 16 (1.5 mg, 1.7 μmol) was taken up in DMSO(50 μl) and QSY21-NHS (1.39 mg, 1.7 μmol, 1 equiv.) and DiPEA (1.5 μl,8.5 μmol, 5 equiv.) were added. After 1 hr the QSY21 amide was purifiedby HPLC (preparatory reverse phase C18 column, CH₃CN/H₂O 0.1% TFA, 40:60to 80:20 over 20 min; 5 mL/min), followed by lyophilization. To removethe Boc protective group the resulting dark blue powder was taken up inTFA/DCM (1/1) and reacted for 30 min, before coevaporation with toluene(3×) to give 0.86 mg of the corresponding TFA salt (0.6 μmol, 35%isolated yield over 2 steps). The amine was dissolved in DMSO (50 μl)and Cy5-NHS (0.5 mg, 0.66 μmol, 1.1 equiv.) and DiPEA (0.57 μl, 3.3μmol, 5 equiv.) were added. After 1 hr, purification by HPLC(preparatory reverse phase C₁₈ column, CH₃CN/H₂O 0.1% TFA, 40:60 to75:25 over 20 min; 5 mL/min), followed by lyophilization afforded probe3 as a dark blue powder (0.67 mg, 0.34 μmol, 57%).

Probe 4 (BMV146). Intermediate 16 (1.0 mg, 1.2 μmol) was taken up inDMSO (50 μl) and Sulfo-QSY21-NHS (1.25 mg, 1.2 μmol, 1 equiv.) and DiPEA(1.05 μl, 6 μmol, 5 equiv.) were added. After 1 hr the Sulfo-QSY21 amidewas purified by HPLC (preparatory reverse phase C₁₈ column, CH₃CN/H₂O0.1% TFA, 20:80 to 80:20 over 20 min; 5 mL/min), followed bylyophilization. To remove the Boc protective group the resulting darkblue powder was taken up in TFA/DCM (1/1) and reacted for 30 min, beforecoevaporation with toluene (3×) to give 1.06 mg of the corresponding TFAsalt (0.66 μmol, 55% over 2 steps). The amine was dissolved in DMSO (50μl) and Cy5-NHS (0.55 mg, 0.73 μmol, 1.1 equiv.) and DiPEA (0.64 μl,3.65 μmol, 5 equiv.) were added. After 1 hr, purification by HPLC(preparatory reverse phase C₁₈ column, CH₃CN/H₂O 0.1% TFA, 15:85 to50:50 over 20 min; 5 mL/min), followed by lyophilization afforded probe4 as a dark blue powder (0.63 mg, 0.3 μmol, 45%).

Probe 5 (BMV118). Intermediate 17 (1.2 mg, 1.3 μmol) was taken up inDMSO (50 μl) and QSY21-NHS (1.0 mg, 1.3 μmol, 1 equiv.) and DiPEA (1.13μl, 6.5 μmol, 5 equiv.) were added. After 2 hr the QSY21 amide waspurified by HPLC (preparatory reverse phase C₁₈ column, CH₃CN/H₂O 0.1%TFA, 40:60 to 80:20 over 20 min; 5 mL/min), followed by lyophilization.To remove the Boc protective group the resulting dark blue powder wastaken up in TFA/DCM (1/1) and reacted for 30 min, before coevaporationwith toluene (3×) to give 2.0 mg of the corresponding TFA salt (1.3μmol, quantitative over 2 steps). The amine was dissolved in DMSO (50μl) and Cy5-NHS (1.0 mg, 1.3 μmol, 1 equiv.) and DiPEA (1.1 μl, 6.5μmol, 5 equiv.) were added. After 1 hr, purification by HPLC(preparatory reverse phase C₁₈ column, CH₃CN/H₂O 0.1% TFA, 40:60 to85:15 over 20 min; 5 mL/min), followed by lyophilization afforded probe5 as a dark blue powder (1.91 mg, 0.94 μmol, 72%).

Probe 6 (BMV119). Intermediate 17 (1.2 mg, 1.3 μmol) was taken up inDMSO (50 μl) and Sulfo-QSY21-NHS (1.35 mg, 1.3 μmol, 1 equiv.) and DiPEA(1.13 μl, 6.5 μmol, 5 equiv.) were added. After 1 hr the Sulfo-QSY21amide was purified by HPLC (preparatory reverse phase C₁₈ column,CH₃CN/H₂O 0.1% TFA, 30:70 to 90:10 over 20 min; 5 mL/min), followed bylyophilization. To remove the Boc protective group the resulting darkblue powder was taken up in TFA/DCM (1/1) and reacted for 30 min, beforecoevaporation with toluene (3×) to give 1.98 mg of the corresponding TFAsalt (0.9 μmol, 70% over 2 steps). The amine was dissolved in DMSO (50μl) and Cy5-NHS (0.7 mg, 0.9 μmol, 1.1 equiv.) and DiPEA (0.8 μl, 4.5μmol, 5 equiv.) were added. After 1 hr, purification by HPLC(preparatory reverse phase C₁₈ column, CH₃CN/H₂O 0.1% TFA, 15:85 to50:50 over 20 min; 5 mL/min), followed by lyophilization afforded probe6 as a dark blue powder (1.63 mg, 0.74 μmol, 82%).

Probe 7 (BMV108). Intermediate 18 (1.2 mg, 1.3 μmol) was taken up inDMSO (50 μl) and QSY21-NHS (1.2 mg, 1.4 μmol, 1.1 equiv.) and DiPEA(1.13 μl, 6.5 μmol, 5 equiv.) were added. After 1 hr the QSY21 amide waspurified by HPLC (preparatory reverse phase C₁₈ column, CH₃CN/H₂O 0.1%TFA, 30:70 to 70:30 over 20 min; 5 mL/min), followed by lyophilizationto afford a dark blue powder (1.43 mg, 0.99 μmol, 76%). The Bocprotective group was subsequently removed in TFA/DCM (1/1) for 30 min,before coevaporation with toluene (3×). The TFA salt was dissolved inDMSO (50 μl) and Cy5-NHS (0.83 mg, 1.1 μmol, 1.1 equiv.) and DiPEA (0.88μl, 5 μmol, 5 equiv.) were added. After 1 hr, purification by HPLC(preparatory reverse phase C₁₈ column, CH₃CN/H₂O 0.1% TFA, 30:70 to70:30 over 20 min; 5 mL/min), followed by lyophilization afforded probe7 as a dark blue powder (0.95 mg, 0.48 μmol, 49% over 2 steps).

Probe 8 (BMV109). Intermediate 18 (5.8 mg, 6.5 μmol) was dissolved inDMSO (100 μl). Sulfo-QSY21-NHS (9.75 mg, 10.39 μmol, 1.6 equiv.) andDiPEA (8.4 μl, 50.5 μmol, 7.8 equiv.) were added and the mixture wasstirred overnight. The Sulfo-QSY21 amide was purified by HPLC(preparatory reverse phase C₁₈ column, CH₃CN/H₂O 0.1% TFA, 25:75 to55:45 over 20 min; 5 mL/min), followed by lyophilization to afford adark blue powder. The Boc protective group was subsequently removed inTFA/DCM (1/1) for 30 min, before coevaporation with toluene (3×). Theresidue was dissolved in DMSO (250 μl) and Cy5-NHS (10.5 mg, 13.9 μmol,2.1 equiv.) and DiPEA (12 μl, 72 μmol, 11 equiv.) were added. After 4hr, purification by HPLC (preparatory reverse phase C₁₈ column,CH₃CN/H₂O 0.1% TFA, 25:75 to 45:55 over 20 min; 5 mL/min), followed bylyophilization afforded probe 8 as a dark blue powder (7.74 mg, 4.61μmol, 71% over 3 steps). ¹H NMR (600 MHz, CD₃CN) δ8.12-8.08 (m, 1H),8.01-7.93 (m, 2H), 7.89-7.85 (m, 2H), 7.75 (dd, J=12.0, 1.5 Hz, 2H),7.72 (dd, J=8.4, 1.7 Hz, 1H), 7.69 (dd, J=8.3, 1.2 Hz, 1H), 7.66 (s,2H), 7.62-7.57 (m, 2H), 7.51 (dd, J=8.4, 5.1 Hz, 2H), 7.46 (d, J=9.4 Hz,2H), 7.41-7.35 (m, 3H), 7.24 (s, 1H), 7.22 (s, 1H), 7.21-7.14 (m, 6H),7.13-7.09 (m, 6H), 7.05 (dd, J=8.8, 4.6 Hz, 1H), 6.39 (t, J=12.8 Hz,1H), 6.11 (t, J=12.6 Hz, 1H), 4.87 (q, J=12.7 Hz, 2H), 4.83 (dd, J=39.7,14.1 Hz, 2H), 4.23-4.12 (m, 4H), 3.93 (q, J=7.2 Hz, 2H), 3.86 (t, J=7.4Hz, 2H), 3.34 (dd, J=6.7, 4.1 Hz, 2H), 3.28-3.15 (m, 9H), 3.04-2.92 (m,3H), 2.80-2.74 (m, 1H), 2.45 (t, J=11.9 Hz, 2H), 2.15-2.09 (m, 1H),2.09-2.03 (m, 2H), 1.74-1.58 (m, 7H), 1.57 (s, 6H), 1.55 (s, 6H), 1.49(dd, J=15.1, 7.4 Hz, 4H), 1.35-1.22 (m, 7H), 1.20 (t, J=7.3 Hz, 3H),1.16-1.12 (m, 4H).

Cell Culture and Labeling of Living Cells and Cell Lysates

RAW cells were cultured in DMEM (GIBCO) supplemented with 10% fetalbovine serum (FBS; GIBCO), 100 units/mL penicillin and 100 μg/mLstreptomycin (GIBCO). 4T1 cells (ATCC) were cultured in RPMI (GIBCO)supplemented with 10% fetal bovine serum (FBS; GIBCO), 100 units/mLpenicillin and 100 μg/mL streptomycin (GIBCO). All cells were culturedin a 5% CO₂ humidified incubator at 37° C. For intact cell labeling,cells were exposed to probe (500× in DMSO) in culture media andincubated for 2 hr at 37° C., unless stated otherwise. Where indicatedthe cells were preincubated for 1 hr with the inhibitor JPM-OEt (500× inDMSO) or exposed to mouse serum (1 μl probe stock solution in DMSO addedto 9 μl serum) for 4 hr before addition to the cells. After labeling,the cells were washed with PBS and resuspended in hypotonic lysis buffer(50 mM PIPES pH 7.4, 10 mM KCl, 5 mM MgCl₂, 2 mM EDTA, 4 mM DTT, and 1%NP-40) and put on ice for 15 min, centrifuged at 4° C. for 30 min andsupernatants were collected, and protein concentration was determinedusing a BCA kit (pierce). 40 μg total protein was denatured be additionof 4×SDS-sample buffer and heating for 3 min at 100° C., resolved bySDS-PAGE (15%) and labeled proteases were visualized by scanning the gelwith a Typhoon imager (GE Healthcare). Labeling intensities werequantified using Image J software. For cathepsin labeling in celllysates, cells were harvested, washed with PBS and resuspended incitrate buffer (50 mM Citrate buffer pH 5.5, 5 mM DDT, 0.5% CHAPS, 0.1%Triton X). After 15 min on ice and centrifugation at 4° C. for 30 minthe supernatants were collected, and protein concentration wasdetermined using a BCA kit (pierce). 40 μg total protein was exposed tothe indicated probe (200× in DMSO) for 1 hr at 37° C. 4×SDS-samplebuffer was added and the protein was denatured for 3 min at 100° C. andanalyzed as described above. For live cell microscopy RAW cells wereseeded in phenol red-free complete medium at a density of 1.10⁵ cells in35 mm glass bottom dish (in vitro scientific) and were culturedovernight. The cells were either exposed to DMSO or 1 μM probe (500× inDMSO) for 2 hours. For the last hr, Lysotracker-green (200 nM finalconcentration, 1000× in DMSO) was added to the cells. Where indicatedthe cells were preincubated for 1 hr with the inhibitor JPM-OEt (500× inDMSO). Cells were imaged at 40× using a Zeiss Axiovert 200 M confocalmicroscope in both Cy5 and FITC channels.

Animal Models

All animal care and experimentation was conducted in accord with currentNational Institutes of Health and Stanford University InstitutionalAnimal Care and Use Committee guidelines. Female BALB/c mice (6-8 weeks,The Jackson Laboratory) were injected in fat pad number 2 and 7 with1.10⁵ 4T1 cells (ATCC) in PBS under isoflurane anesthesia and tumorgrowth was monitored. 24 hr before imaging the hair on the region ofinterest was removed using ‘Nair lotion’. On day 10, the indicated probe(20 nmol; 0.8 nmol g⁻¹) was administered via tail vein in 100 μL, volume(20% DMSO in PBS). After injection, mice were imaged noninvasively atindicated time points using an IVIS 100 system (Xenogen). The imageswere analyzed with Living Image software (PerkinElmer). After the lasttime point the mice were anesthetized with isofluorane and killed bycervical dislocation. For ex vivo fluorescence measurements andassessment of in vivo probe labeling profile tumors were removed, imagedusing an FMT 2500 (PerkinElmer) and the tissue was sonicated (1 min onice) in citrate buffer (50 mM Citrate buffer pH 5.5, 5 mM DDT, 0.5%CHAPS, 0.1% Triton X). After centrifugation at 4° C. for 30 min thesupernatants were collected, and protein concentration was determinedusing a BCA kit (pierce). 40 μg total protein was denatured inSDS-sample buffer for 3 min at 100° C. and analyzed as described above.For immunofluorescence the resected tumors were incubated in a 4% PFAsolution in PBS for 6 hr at 4° C. followed by overnight overnightincubation in a 30% sucrose solution and freezing fo the tissue in OCTmedium. 6-μm sections were fixed in acetone, blocked with PNB blockingbuffer and incubated with rat anti-mouse CD68 (1:1000; Serotec)overnight. Goat-anti Rat conjugated with AlexaFluor-488 (1:500;Invitrogen) was incubated for 1 hr at room temperature. Sections werethen stained with DAPI (2 μg/mL; Invitrogen) for five minutes and thenmounted in ProLong Gold Mounting Medium (Invitrogen). Tissues were thenvisualized using a Zeiss Axiovert 200M microscope.

All patents, patent publications, and other published referencesmentioned herein are hereby incorporated by reference in theirentireties as if each had been individually and specificallyincorporated by reference herein.

While specific examples have been provided, the above description isillustrative and not restrictive. Any one or more of the features of thepreviously described embodiments can be combined in any manner with oneor more features of any other embodiments in the present invention.Furthermore, many variations of the invention will become apparent tothose skilled in the art upon review of the specification. The scope ofthe invention should, therefore, be determined by reference to theappended claims, along with their full scope of equivalents.

1. A compound for use in labeling a protease having the formula (I):

wherein L is an ether-linked leaving element, wherein L comprises aquencher; D-T- is

wherein L₁ is a linker; AA₁ is an amino acid side chain; U is O, N, orS; R₁ is alkyl, alkenyl, alkynyl, aryl, aralkyl, heteroaryl,heteroaralkyl, cycloalkyl, cycloalkenyl, cycloalkylalkyl, heterocyclyl,heterocyclylalkyl, or a protecting group, and is optionally substitutedwith 1 to 3 A groups; and each A is independently alkyl, alkenyl,alkynyl, alkoxy, alkanoyl, alkylamino, aryl, aryloxy, arylamino,aralkyl, aralkoxy, aralkanoyl, aralkamino, heteroaryl, heteroaryloxy,heteroarylamino, heteroaralkyl, heteroaralkoxy, heteroaralkanoyl,heteroaralkamino, cycloalkyl, cycloalkenyl, cycloalkylalkyl,cycloalkoxy, cycloalkanoyl, cycloalkamino, heterocyclyl,heterocyclyloxy, heterocyclylamino, heterocyclylalkyl,heterocyclylalkoxy, heterocyclylalkanoyl, heterocyclylalkamino,hydroxyl, thio, amino, alkanoylamino, aroylamino, aralkanoylamino,alkylcarboxy, carbonate, carbamate, guanidinyl, urea, halo,trihalomethyl, cyano, nitro, phosphoryl, sulfonyl, sulfonamido, orazido; and D is a fluorescent label. 2-3. (canceled)
 4. The compound ofclaim 1, wherein the fluorescent label is a fluorescein, an Oregongreen, a bora-diaza-indecene, a rhodamine, or a cyanine label.
 5. Thecompound of claim 4, wherein the fluorescent label is a cyanine label.6. The compound of claim 5, wherein the cyanine label is Cy5.
 7. Thecompound of claim 1, wherein T targets the compound to a cysteineprotease. 8-12. (canceled)
 13. The compound of claim 1, wherein L₁ is anoptionally substituted alkyl linker, wherein each carbon atom isoptionally replaced with a heteroatom.
 14. The compound of claim 1,wherein AA₁ is an aralkyl amino acid side chain, optionally substitutedwith 1 to 3 A groups.
 15. The compound of claim 1, wherein U is O.16-21. (canceled)
 22. The compound of claim 1, wherein L is L₂-L₃-Q; L₂is a phenoxy group; L₃ is a linker; and Q is a quencher.
 23. Thecompound of claim 22, wherein L is

wherein each Y is independently an electron-withdrawing group orhydrogen.
 24. The compound of claim 23, wherein each Y is independentlya halogen or hydrogen.
 25. The compound of claim 24, wherein L is

and L₃ is an optionally substituted alkyl linker, wherein each carbonatom is optionally replaced with a heteroatom.
 26. The compound of claim25, wherein L is

R is a QSY quencher; and n is an integer from 1 to
 16. 27. The compoundof claim 26, wherein the QSY quencher is a hydrophilic QSY quencher. 28.The compound of claim 27, wherein the hydrophilic QSY quencher is asulfo-QSY quencher. 29-30. (canceled)
 31. The compound of claim 26,wherein R is QSY21 or sulfo-QSY21, and D is Cy5.
 32. (canceled)
 33. Acomposition for use in labeling a protease in an animal comprising acompound of claim 1 and a pharmaceutically acceptable carrier.
 34. Amethod of labeling a protease in an animal comprising the step of:administering the composition of claim 33 to the animal.
 35. A method ofvisualizing a tumor in an animal comprising the steps of: administeringthe composition of claim 33 to the animal; and measuring a detectablesignal generated in the animal from a reaction of the composition with acathepsin cysteine protease; wherein the detectable signal is associatedwith a tumor in the animal.
 36. The method of claim 35, wherein thedetectable signal is a fluorescent signal.
 37. The method of claim 36,wherein the fluorescent signal is generated at a tumor margin.
 38. Thecompound of claim 1, wherein the fluorescent label is an infrared dye.39. The compound of claim 38, wherein the fluorescent label is selectedfrom the group consisting of IRDye 800CW, IRDye 680RD, IRDye 680LT,IRDye 750, IRDye 700DX, IRDye 800RS, and IRDye
 650. 40. The compound ofclaim 1, wherein the quencher is a QSY quencher.
 41. The compound ofclaim 1, wherein the quencher is IRDye QC-1.